US9714940B2 - NMR systems and methods for the rapid detection of analytes - Google Patents

NMR systems and methods for the rapid detection of analytes Download PDF

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US9714940B2
US9714940B2 US13/384,051 US201113384051A US9714940B2 US 9714940 B2 US9714940 B2 US 9714940B2 US 201113384051 A US201113384051 A US 201113384051A US 9714940 B2 US9714940 B2 US 9714940B2
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magnetic particles
sample
nucleic acid
particles
magnetic
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US20130260367A1 (en
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Thomas Jay Lowery, JR.
Mark John Audeh
Matthew Blanco
James Franklin Chepin
Vasiliki Demas
Rahul Dhanda
Lori Anne Neely
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T2 Biosystems Inc
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Definitions

  • This invention features assays and devices for the detection of analytes, and their use in the treatment and diagnosis of disease.
  • Magnetic sensors have been designed to detect molecular interactions in a variety of media, including biofluids, food products, and soil samples, among other media. Upon target binding, these sensors cause changes in properties of neighboring water molecules (or any solvent molecule with free hydrogens) of a sample, which can be detected by magnetic resonance (NMR/MRI) techniques.
  • NMR/MRI magnetic resonance
  • magnetic sensors are magnetic particles that bind or otherwise link to their intended molecular target to form clusters (aggregates). It is believed that when magnetic particles assemble into clusters and the effective cross sectional area becomes larger (and the cluster number density is smaller), the interactions with the water or other solvent molecules are altered, leading to a change in the measured relaxation rates (e.g., T 2 , T 1 , T 2 *), susceptibility, frequency of precession, among other physical changes. Additionally, cluster formation can be designed to be reversible (e.g., by temperature shift, chemical cleavage, pH shift, etc.) so that “forward” or “reverse” (competitive and inhibition) assays can be developed for detection of specific analytes.
  • the invention features systems and methods for the detection of analytes.
  • the invention features a method for detecting the presence of an analyte in a liquid sample, the method including: (a) contacting a solution with magnetic particles to produce a liquid sample including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 699 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, or from 500 to 699 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1 ⁇ 10 8 to 1 ⁇ 10 9
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the analyte can be creatinine
  • the liquid sample can include a multivalent binding agent bearing a plurality of creatinine conjugates
  • the magnetic particles can include a surface decorated with creatinine antibodies.
  • the analyte can be tacrolimus
  • the liquid sample can include a multivalent binding agent bearing a plurality of tacrolimus conjugates
  • the magnetic particles can include a surface decorated with tacrolimus antibodies.
  • step (d) includes measuring the T 2 relaxation response of the liquid sample, and wherein increasing agglomeration in the liquid sample produces an increase in the observed T 2 relaxation rate of the sample.
  • the analyte is a target nucleic acid (e.g., a target nucleic acid extracted from a leukocyte, or a pathogen).
  • the invention features a method for detecting the presence of an analyte in a liquid sample, the method including (a) contacting a solution with magnetic particles to produce a liquid sample including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 19 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 700 nm to 1200 nm (e.g., from 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 9 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1 ⁇ 10 9 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 ,
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the analyte can be creatinine
  • the liquid sample can include a multivalent binding agent bearing a plurality of creatinine conjugates
  • the magnetic particles can include a surface decorated with creatinine antibodies.
  • the analyte can be tacrolimus
  • the liquid sample can include a multivalent binding agent bearing a plurality of tacrolimus conjugates
  • the magnetic particles can include a surface decorated with tacrolimus antibodies.
  • step (d) includes measuring the T 2 relaxation response of the liquid sample, and wherein increasing agglomeration in the liquid sample produces an increase in the observed T 2 relaxation rate of the sample.
  • the analyte is a target nucleic acid (e.g., a target nucleic acid extracted from a leukocyte, or a pathogen).
  • the invention further features a method for detecting the presence of a pathogen in a whole blood sample, the method including: (a) providing a whole blood sample from a subject; (b) mixing the whole blood sample with an erythrocyte lysis agent solution to produce disrupted red blood cells; (c) following step (b), centrifuging the sample to form a supernatant and a pellet, discarding some or all of the supernatant, and resuspending the pellet to form an extract, optionally washing the pellet (e.g., with TE buffer) prior to resuspending the pellet and optionally repeating step (c); (d) lysing cells of the extract to form a lysate; (e) placing the lysate of step (d) in a detection tube and amplifying a target nucleic acid in the lysate to form an amplified lysate solution including the target nucleic acid, wherein the target nucleic acid is characteristic of the pathogen to be detected; (f) following step
  • steps (a) through (i) are completed within 4 hours (e.g., within 3.5 hours, 3.0 hours, 2.5 hours, 2 hours, 1.5 hours, or 1 hour).
  • step (i) is carried out without any prior purification of the amplified lysate solution (i.e., the lysate solution is unfractionated after it is formed).
  • step c includes washing the pellet prior to resuspending the pellet to form the extract.
  • step (d) includes combining the extract with beads to form a mixture and agitating the mixture to form a lysate.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the lysate further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the lysate can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the invention features a method for detecting the presence of a target nucleic acid in a whole blood sample, the method including: (a) providing one or more cells from a whole blood sample from a subject; (b) lysing the cells to form a lysate; (c) amplifying a target nucleic acid in the lysate to form an amplified lysate solution comprising the target nucleic acid; (d) following step (c), adding to a detection tube the amplified lysate solution and from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the amplified lysate solution, wherein the magnetic particles have a mean diameter of from 700 nm to 1200 nm and binding moieties on their surface, the binding moieties operative to alter aggregation of the magnetic particles in the presence of the target nucleic acid or a multivalent binding agent; (e) placing the detection tube in a device, the device including a support defining a well for holding the detection tube including the magnetic
  • step (b) includes combining the extract with beads to form a mixture and agitating the mixture to form a lysate.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the lysate further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.
  • the magnetic particles optionally include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the lysate can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the invention further features a method for detecting the presence of a target nucleic acid in a whole blood sample, the method including: (a) providing an extract produced by lysing the red blood cells in a whole blood sample from a subject, centrifuging the sample to form a supernatant and a pellet, discarding some or all of the supernatant, and resuspending the pellet to form an extract, optionally washing the pellet (e.g., with TE buffer) prior to resuspending the pellet and optionally repeating the centrifuging, discarding, and washing of step (a); (b) lysing cells in the extract to form a lysate; (c) placing the lysate of step (b) in a detection tube and amplifying nucleic acids therein to form an amplified lysate solution including from 40% (w/w) to 95% (w/w) the target nucleic acid (e.g., from 40 to 60%, from 60 to 80%, or from 85 to 95% (
  • step (b) includes combining the extract with beads to form a mixture and agitating the mixture to form a lysate.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the lysate further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the lysate can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the invention features a method for detecting the presence of a Candida species in a liquid sample, the method including: (a) lysing the Candida cells in the liquid sample; (b) amplifying a nucleic acid to be detected in the presence of a forward primer and a reverse primer, each of which is universal to multiple Candida species to form a solution including a Candida amplicon; (c) contacting the solution with magnetic particles to produce a liquid sample including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 700 nm to 1200 nm (e.g., from 700 to 850, 800 to 950, 900 to 1050, or
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the forward primer can include, for example, the sequence 5′-GGC ATG CCT GTT TGA GCG TC-3′ (SEQ ID NO. 1).
  • the reverse primer can include, for example, the sequence 5′-GCT TAT TGA TAT GCT TAA GTT CAG CGG GT-3′ (SEQ ID NO. 2).
  • the Candida species is Candida albicans
  • the first probe includes the oligonucleotide sequence 5′-ACC CAG CGG TTT GAG GGA GAA AC-3′ (SEQ ID NO. 3)
  • the second probe includes the oligonucleotide sequence 5′-AAA GTT TGA AGA TAT ACG TGG TGG ACG TTA-3′ (SEQ ID NO.
  • the Candida species is Candida krusei and the first probe and the second probe include an oligonucleotide sequence selected from: 5′-CGC ACG CGC AAG ATG GAA ACG-3′ (SEQ ID NO. 5), 5′-AAG TTC AGC GGG TAT TCC TAC CT-3′ (SEQ ID NO. 6), and 5′-AGC TTT TTG TTG TCT CGC AAC ACT CGC-3′ (SEQ ID NO. 32); (iii) the Candida species is Candida glabrata , the first probe includes the oligonucleotide sequence: 5′-CTA CCA AAC ACA ATG TGT TTG AGA AG-3′ (SEQ ID NO.
  • the second probe includes the oligonucleotide sequence: 5′-CCT GAT TTG AGG TCA AAC TTA AAG ACG TCT G-3′ (SEQ ID NO. 8); and (iv) the Candida species is Candida parapsilosis or Candida tropicalis and the first probe and the second probe include an oligonucleotide sequence selected from: 5′-AGT CCT ACC TGA TTT GAG GTCNitIndAA-3′ (SEQ ID NO. 9), 5′-CCG NitIndGG GTT TGA GGG AGA AAT-3′ (SEQ ID NO. 10), AAA GTT ATG AAATAA ATT GTG GTG GCC ACT AGC (SEQ ID NO.
  • steps (a) through (h) are completed within 4 hours (e.g., within 3.5 hours, 3.0 hours, 2.5 hours, 2 hours, 1.5 hours, or 1 hour or less).
  • the magnetic particles include two populations, a first population bearing the first probe on its surface, and the second population bearing the second probe on its surface.
  • the magnetic particles are a single population bearing both the first probe and the second probe on the surface of the magnetic particles.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the Candida amplicon and the second probe operative to bind to a second segment of the Candida amplicon, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the Candida amplicon.
  • the method can produce (i) a coefficient of variation in the T2 value of less than 20% on Candida positive samples; (ii) at least 95% correct detection at less than or equal to 5 cells/mL in samples spiked into 50 individual healthy patient blood samples; (iii) at least 95% correct detection less than or equal to 5 cells/mL in samples spiked into 50 individual unhealthy patient blood samples; and/or (iv) greater than or equal to 80% correct detection in clinically positive patient samples (i.e., Candida positive by another technique, such as by cell culture) starting with 2 mL of blood.
  • clinically positive patient samples i.e., Candida positive by another technique, such as by cell culture
  • the invention features a method for detecting the presence of a Candida species in a whole blood sample sample, the method including: (a) providing an extract produced by lysing the red blood cells in a whole blood sample from a subject; (b) centrifuging the sample to form a supernatant and a pellet, discarding some or all of the supernatant; (c) washing the pellet (e.g., with TE buffer) by mixing the pellet with a buffer, agitating the sample (e.g., by vortexing), centrifuging the sample to form a supernatant and a pellet, discarding some or all of the supernatant; (d) optionally repeating steps (b) and (c); (e) bead beating the pellet to form a lysate in the presence of a buffer (e.g., TE buffer); (f) centrifuging the sample to form a supernatant containing the lysate; (g) amplifying nucleic acids in the lysate of step
  • the invention features a method for detecting the presence of a pathogen in a whole blood sample, the method including the steps of: (a) providing from 0.05 to 4.0 mL of the whole blood sample (e.g., from 0.05 to 0.25, 0.25 to 0.5, 0.25 to 0.75, 0.4 to 0.8, 0.5 to 0.75, 0.6 to 0.9, 0.65 to 1.25, 1.25 to 2.5, 2.5 to 3.5, or 3.0 to 4.0 mL of whole blood); (b) placing an aliquot of the sample of step (a) in a container and amplifying a target nucleic acid in the sample to form an amplified solution including the target nucleic acid, wherein the target nucleic acid is characteristic of the pathogen to be detected; (c) placing the amplified liquid sample in a detecting device; (d) on the basis of the result of step (c), detecting the pathogen, wherein the pathogen is selected from bacteria and fungi, and wherein the method is capable of detecting a pathogen concentration of
  • the detecting device can detect the pathogen via an optical, fluorescent, mass, density, magnetic, chromatographic, and/or electrochemical measurement of the amplified liquid sample.
  • steps (a) through (d) are completed within 3 hours (e.g., within 3.2, 2.9, 2.7, 2.5, 2.3, 2.2, 2.1, 2.0, 1.9, 1.8, 1.7, 1.6, or 1.5 hours or 1 hour).
  • step (c) is carried out without any prior purification of the amplified solution, and/or the liquid sample of step (c) includes whole blood proteins and non-target oligonucleotides.
  • the pathogen is selected from bacteria and fungi.
  • the pathogen can be any bacterial or fungal pathogen described herein.
  • the invention also features a method for detecting the presence of a pathogen in a whole blood sample, the method including the steps of: (a) providing a whole blood sample from a subject; (b) mixing from 0.05 to 4.0 mL of the whole blood sample (e.g., from 0.05 to 0.25, 0.25 to 0.5, 0.25 to 0.75, 0.4 to 0.8, 0.5 to 0.75, 0.6 to 0.9, 0.65 to 1.25, 1.25 to 2.5, 2.5 to 3.5, or 3.0 to 4.0 mL of whole blood) with an erythrocyte lysis agent solution to produce disrupted red blood cells; (c) following step (b), centrifuging the sample to form a supernatant and a pellet, discarding some or all of the supernatant, and resuspending the pellet to form an extract, optionally washing the pellet (e.g., with TE buffer) prior to resuspending the pellet and optionally repeating step (c); (d) lysing cells of the extract to form
  • steps (a) through (i) are completed within 3 hours (e.g., within 3.2, 2.9, 2.7, 2.5, 2.3, 2.2, 2.1, 2.0, 1.9, 1.8, 1.7, 1.6, 1.5, or for less hours).
  • step (i) is carried out without any prior purification of the amplified lysate solution, and/or the liquid sample of step (i) includes whole blood proteins and non-target oligonucleotides.
  • the pathogen is selected from bacteria and fungi.
  • the pathogen can be any bacterial or fungal pathogen described herein.
  • the method is capable of measuring a pathogen concentration of 10 cells/mL in the whole blood sample with a coefficient of variation of less than 15% (e.g., 10 cells/mL with a coefficient of variation of less than 15%, 10%, 7.5%, or 5%; or 25 cells/mL with a coefficient of variation of less than 15%, 10%, 7.5%, or 5%; or 50 cells/mL with a coefficient of variation of less than 15%, 10%, 7.5%, or 5%; or 100 cells/mL with a coefficient of variation of less than 15%, 10%, 7.5%, or 5%).
  • a coefficient of variation of less than 15% e.g., 10 cells/mL with a coefficient of variation of less than 15%, 10%, 7.5%, or 5%
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the method for monitoring can include any of the magnetic assisted agglomeration methods described herein.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid.
  • the invention further features a method for detecting the presence of a virus in a whole blood sample, the method including the steps of: (a) providing a plasma sample from a subject; (b) mixing from 0.05 to 4.0 mL of the plasma sample (e.g., from 0.05 to 0.25, 0.25 to 0.5, 0.25 to 0.75, 0.4 to 0.8, 0.5 to 0.75, 0.6 to 0.9, 0.65 to 1.25, 1.25 to 2.5, 2.5 to 3.5, or 3.0 to 4.0 mL of whole blood) with a lysis agent to produce a mixture comprising disrupted viruses; (c) placing the mixture of step (b) in a container and amplifying a target nucleic acid in the filtrate to form an amplified filtrate solution including the target nucleic acid, wherein the target nucleic acid is characteristic of the virus to be detected; (d) following step (c), mixing the amplified filtrate solution with from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the amplified filtrate
  • steps (a) through (g) are completed within 3 hours (e.g., within 3.2, 2.9, 2.7, 2.5, 2.3, 2.2, 2.1, 2.0, 1.9, 1.8, 1.7, 1.6, 1.5 hours, or 1 hour or less).
  • the virus can be any viral pathogen described herein.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the method for monitoring can include any of the magnetic assisted agglomeration methods described herein.
  • the magnetic particles can include one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid.
  • the assay can be a disaggregation assay in which the magnetic particles include a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety including a first probe and a second probe, the first probe operative to bind to the first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid.
  • the PCR method can be real time PCR for quantifying the amount of a target nucleic acid present in a sample.
  • the invention features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule (e.g., using PCR or isothermal amplification) in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule, wherein the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) biotin labeled amplification primers specific for the target nucleic acid molecule, and (3) avidin labeled superparamagnetic particles.
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) biotin labeled amplification primers specific for the target nucleic acid molecule, and (3) avidin labeled superparamagnetic particles.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • the amplification includes the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the PCR.
  • the invention further features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule (e.g., using PCR or isothermal amplification) in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule.
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) amplification primers including a 5′ overhang, wherein the amplification primers are specific for the target nucleic acid molecule, and (3) oligonucleotide labeled superparamagnetic particles, wherein the oligonucleotide label is substantially complementary to the 5′ overhang of the amplification primers.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • the amplification includes the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the amplification.
  • the invention further features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule (e.g., using PCR or isothermal amplification) in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule.
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) amplification primers specific for the target nucleic acid molecule, and (3) oligonucleotide labeled superparamagnetic particles, wherein the oligonucleotide label contains a hairpin structure and a portion of the hairpin structure is substantially complementary to a portion of the nucleic acid sequence of the amplicons.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • This amplification of this method includes the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the amplification.
  • the invention also features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule using PCR in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule.
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) a polymerase with 5′ exonuclease activity, (3) amplification primers specific for the target nucleic acid molecule, and (4) oligonucleotide tethered superparamagnetic particles, wherein the oligonucleotide tether connects at least two superparamagnetic particles and the oligonucleotide tether is substantially complementary to a portion of the nucleic acid sequence of the amplicons.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • the amplification of this method includes the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the PCR.
  • the invention also features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule (e.g., using PCR or isothermal amplification) in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule.
  • amplifying the target nucleic acid molecule e.g., using PCR or isothermal amplification
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) amplification primers specific for the target nucleic acid molecule, and (3) superparamagnetic particles labeled with a plurality of oligonucleotides, wherein a first group of the plurality of oligonucleotides are substantially complementary to a portion of the nucleic acid sequence of the amplicons and substantially complementary to a second group of the plurality of oligonucleotides, wherein the first group of the plurality of oligonucleotides has a lesser hybridization affinity for the second group of the plurality of oligonucleotides than for the amplicons.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • the amplification of this method includes the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the amplification.
  • the invention further features a method of quantifying a target nucleic acid molecule in a sample by amplifying the target nucleic acid molecule (e.g., using PCR or isothermal amplification) in an amplification reaction mixture in a detection tube resulting in the production of amplicons corresponding to the target nucleic acid molecule.
  • the amplification reaction mixture includes (1) a target nucleic acid molecule, (2) amplification primers specific for the target nucleic acid molecule, and (3) superparamagnetic particles.
  • the amplification is performed in a device including a support defining a well for holding the detection tube including the superparamagnetic particles and the target nucleic acid molecule, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the sample to a bias magnetic field created using one or more magnets and an RF pulse sequence.
  • the amplification of this method including the following steps:
  • the initial quantity of target nucleic acid molecule in the sample is determined based on the quantity of amplicons determined at each cycle of the amplification.
  • the detection tube can remained sealed throughout the amplification reaction.
  • the superparamagnetic particles of these methods can be greater or less than 100 nm in diameter (e.g., 30 nm in diameter).
  • the methods can further include applying a magnetic field to the detection tube following the measuring the signal from the detection tube, resulting in the sequestration of the superparamagnetic particles to the side of the detection tube, and releasing the magnetic field subsequent to the completion of one or more additional cycles of amplification.
  • the sample can, e.g., not include isolated nucleic acid molecules prior to step (a) (e.g., the sample can be whole blood or not contain a target nucleic acid molecule prior to step (a)).
  • the invention features a method of monitoring one or more analytes in a liquid sample derived from a patient for the diagnosis, management, or treatment of a medical condition in a patient, the method including (a) combining with the liquid sample from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), and a T 2 relaxivity per particle of from 1 ⁇ 10
  • the one or more analytes include creatinine.
  • the patient is immunocompromised, and the one or more analytes include an analyte selected from pathogen-associated analytes, antibiotic agents, antifungal agents, and antiviral agents (e.g., the one or more analytes can include Candida spp., tacrolimus, fluconazole, and/or creatinine).
  • the patient has cancer, and the one or more analytes are selected from anticancer agents, and genetic markers present in a cancer cell.
  • the patient can have, or be at risk of, an infection, and the one or more analytes include an analyte selected from pathogen-associated analytes, antibiotic agents, antifungal agents, and antiviral agents.
  • the patient can have an immunoinflammatory condition, and the one or more analytes include an analyte selected from anti inflammatory agents and TNF-alpha.
  • the patient can have heart disease, and the one or more analytes can include a cardiac marker.
  • the patient can have HIV/AIDS, and the one or more analytes can include CD3, viral load, and AZT.
  • the method is used to monitor the liver function of the patient, and wherein the one or more analytes are selected from albumin, aspartate transaminase, alanine transaminase, alkaline phosphatase, gamma glutamyl transpeptidase, bilirubin, alpha fetoprotein, lactase dehydrogenase, mitochondrial antibodies, and cytochrome P450.
  • the one or more analytes include cytochrome P450 polymorphisms, and the ability of the patient to metabolize a drug is evaluated.
  • the method can include identifying the patient as a poor metabolizer, a normal metabolizer, an intermediate metabolizer, or an ultra rapid metabolizer.
  • the method can be used to determine an appropriate dose of a therapeutic agent in a patient by (i) administering the therapeutic agent to the patient; (ii) following step (i), obtaining a sample including the therapeutic agent or metabolite thereof from the patient; (iii) contacting the sample with the magnetic particles and exposing the sample to the bias magnetic field and the RF pulse sequence and detecting a signal produced by the sample; and (iv) on the basis of the result of step (iii), determining the concentration of the therapeutic agent or metabolite thereof.
  • the therapeutic agent can be an anticancer agent, antibiotic agent, antifungal agent, or any therapeutic agent described herein.
  • the monitoring can be intermittent (e.g., periodic), or continuous.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the method for monitoring can include any of the magnetic assisted agglomeration methods described herein.
  • the invention features a method of diagnosing sepsis in a subject, the method including (a) obtaining a liquid sample derived from the blood of a patient; (b) preparing a first assay sample by combining with a portion of the liquid sample from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 1 or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), and a T 2 relaxivity per particle of
  • the one or more pathogen-associated analytes of the first assay sample are derived from a pathogen associated with sepsis selected from Acinetobacter baumannii, Aspergillus fumigatis, Bacteroides fragilis, B. fragilis , blaSHV, Burkholderia cepacia, Campylobacter jejuni/coli, Candida guilliermondii, C. albicans, C. glabrata, C. krusei, C. lusitaniae, C. parapsilosis, C. tropicalis, Clostridium pefringens , Coagulase negative Staph, Enterobacter aeraogenes, E.
  • a pathogen associated with sepsis selected from Acinetobacter baumannii, Aspergillus fumigatis, Bacteroides fragilis, B. fragilis , blaSHV, Burkholderia cepacia, Campylobacter jejuni/coli, Candida guillier
  • the one or more pathogen-associated analytes can be derived from treatment resistant strains of bacteria, such as penicillin-resistant, methicillin-resistant, quinolone-resistant, macrolide-resistant, and/or vancomycin-resistant bacterial strains (e.g., methicillin resistant Staphylococcus aureus or vancomycin-resistant enterococci).
  • treatment resistant strains of bacteria such as penicillin-resistant, methicillin-resistant, quinolone-resistant, macrolide-resistant, and/or vancomycin-resistant bacterial strains (e.g., methicillin resistant Staphylococcus aureus or vancomycin-resistant enterococci).
  • the one or more analytes of the second assay sample are selected from GRO-alpha, High mobility group-box 1 protein (HMBG-1), IL-1 receptor, IL-1 receptor antagonist, IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, macrophage inflammatory protein (MIP-1), macrophage migration inhibitory factor (MIF), osteopontin, RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), TNF- ⁇ , C-reactive protein (CRP), CD64, and monocyte chemotactic protein 1 (MCP-1).
  • HMBG-1 High mobility group-box 1 protein
  • MIP-1 macrophage inflammatory protein
  • MIF macrophage migration inhibitory factor
  • osteopontin RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5)
  • TNF- ⁇ C-reactive protein
  • CD64 CD64
  • the method further includes preparing a third assay sample to monitor the concentration of an antiviral agent, antibiotic agent, or antifungal agent circulating in the blood stream of the subject.
  • the subject can be an immunocompromised subject, or a subject at risk of becoming immunocompromised.
  • the monitoring can be intermittent (e.g., periodic), or continuous.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the method for monitoring can include any of the magnetic assisted agglomeration methods described herein.
  • the invention further features a method of monitoring one or more analytes in a liquid sample derived from a patient for the diagnosis, management, or treatment of sepsis or SIRS in a patient, the method including: (a) combining with the liquid sample from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), and a T 2 relaxivity per particle
  • the method can include (i) monitoring a pathogen-associated analyte, and (ii) monitoring a second analyte characteristic of sepsis selected from GRO-alpha, High mobility group-box 1 protein (HMBG-1), IL-1 receptor, IL-1 receptor antagonist, IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, macrophage inflammatory protein (MIP-1), macrophage migration inhibitory factor (MIF), osteopontin, RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), TNF- ⁇ , C-reactive protein (CRP), CD64, monocyte chemotactic protein 1 (MCP-1), adenosine deaminase binding protein (ABP-26), inducible nitric oxide synthetase (iNOS), lipopolysaccharide binding protein, and procalcitonin.
  • HMBG-1 High
  • the pathogen-associated analyte is derived from a pathogen associated with sepsis selected from Acinetobacter baumannii, Aspergillus fumigatis, Bacteroides fragilis, B. fragilis , blaSHV, Burkholderia cepacia, Campylobacter jejuni/coli, Candida guilliermondii, C. albicans, C. glabrata, C. krusei, C. Lusitaniae, C. parapsilosis, C. tropicalis, Clostridium pefringens , Coagulase negative Staph, Enterobacter aeraogenes, E.
  • a pathogen associated with sepsis selected from Acinetobacter baumannii, Aspergillus fumigatis, Bacteroides fragilis, B. fragilis , blaSHV, Burkholderia cepacia, Campylobacter jejuni/coli, Candida guilliermondii, C. albi
  • the pathogen-associated analyte can be derived from a treatment resistant strain of bacteria, such as penicillin-resistant, methicillin-resistant, quinolone-resistant, macrolide-resistant, and/or vancomycin-resistant bacterial strains (e.g., methicillin resistant Staphylococcus aureus or vancomycin-resistant enterococci).
  • a treatment resistant strain of bacteria such as penicillin-resistant, methicillin-resistant, quinolone-resistant, macrolide-resistant, and/or vancomycin-resistant bacterial strains (e.g., methicillin resistant Staphylococcus aureus or vancomycin-resistant enterococci).
  • the second analytes is selected from GRO-alpha, High mobility group-box 1 protein (HMBG-1), IL-1 receptor, IL-1 receptor antagonist, IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, macrophage inflammatory protein (MIP-1), macrophage migration inhibitory factor (MIF), osteopontin, RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), TNF- ⁇ , C-reactive protein (CRP), CD64, and monocyte chemotactic protein 1 (MCP-1).
  • HMBG-1 High mobility group-box 1 protein
  • MIP-1 macrophage inflammatory protein
  • MIF macrophage migration inhibitory factor
  • osteopontin RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5)
  • TNF- ⁇ T-reactive protein
  • CD64 C-reactive protein
  • MCP-1 monocyte chemotactic
  • the method further includes preparing a third assay sample to monitor the concentration of an antiviral agent, antibiotic agent, or antifungal agent circulating in the blood stream of the subject.
  • the subject can be an immunocompromised subject, or a subject at risk of becoming immunocompromised.
  • the monitoring can be intermittent (e.g., periodic), or continuous.
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the method for monitoring can include any of the magnetic assisted agglomeration methods described herein.
  • the invention features a method for assisting the specific agglomeration of magnetic particles in a liquid sample, the method including: (i) providing a liquid sample including one or more analytes and the magnetic particles, wherein the magnetic particles have binding moieties on their surfaces, the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent; (ii) exposing the liquid sample to a magnetic field; (iii) removing the liquid sample from the magnetic field; and (iv) repeating step (ii).
  • the invention further features a method for assisting the specific agglomeration of magnetic particles in a liquid sample by (i) providing a liquid sample including one or more analytes and the magnetic particles, wherein the magnetic particles have binding moieties on their surfaces, the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent; (ii) applying a magnetic field gradient to the liquid sample for a time sufficient to cause concentration of the magnetic particles in a first portion of the liquid sample, the magnetic field gradient being aligned in a first direction relative to the liquid sample; (iii) following step (ii), applying a magnetic field to the liquid sample for a time sufficient to cause concentration of the magnetic particles in a second portion of the liquid sample, the magnetic field being aligned in a second direction relative to the liquid sample; and (iv) optionally repeating steps (ii) and (iii).
  • the angle between the first direction and the second direction relative to the liquid sample is between 0° and 180° (e.g., from 0° to 10°, 5° to 120°, 20° to 60°, 30° to 80°, 45° to 90°, 60° to 120°, 80° to 135°, or from 120° to 180°).
  • the invention features a method for assisting the specific agglomeration of magnetic particles in a liquid sample by (i) providing a liquid sample including one or more analytes and the magnetic particles, wherein the magnetic particles have binding moieties on their surfaces, the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent; (ii) applying a magnetic field gradient to the liquid sample for a time sufficient to cause concentration of the magnetic particles in a first portion of the liquid sample; (iii) following step (ii), agitating the liquid sample; and (iv) repeating step (ii).
  • step (iii) includes vortexing the liquid sample, or mixing the sample using any method described herein.
  • the invention also features a method for assisting the specific agglomeration of magnetic particles in a liquid sample by (i) providing a liquid sample including one or more analytes and the magnetic particles, wherein the magnetic particles have binding moieties on their surfaces, the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent; and (ii) exposing the liquid sample to a gradient magnetic field and rotating the gradient magnetic field about the sample, or rotating the sample within the gradient magnetic field. The sample can be rotated slowly.
  • the sample is rotated at a rate of 0.0333 Hz, or less (e.g., from 0.000833 Hz to 0.0333 Hz, from 0.00166 Hz to 0.0333 Hz, or from 0.00333 Hz to 0.0333 Hz).
  • the method further includes (iii) following step (ii), agitating the liquid sample; and (iv) repeating step (ii).
  • the one or more magnets providing the magnetic field gradient within the liquid sample have a maximum field strength of from 0.01 T to 10 T (e.g., from 0.01 T to 0.05 T, 0.05 T to 0.1 T, 0.1 T to 0.5 T, 0.5 T to 1 T, 1 T to 3 T, or from 3 T to 10 T) and wherein the gradient magnetic field varies from 0.1 mT/mm to 10 T/mm across the liquid sample (e.g., from 0.1 mT/mm to 0.5 mT/mm, 0.3 mT/mm to 1 mT/mm, 0.5 mT/mm to 5 mT/mm, 5 mT/mm to 20 mT/mm, 10 mT/mm to 100 mT/mm, 100
  • step (ii) includes applying the magnetic field gradient to the liquid sample for a period of from 1 second to 5 minutes (e.g., from 1 to 20 seconds, from 20 to 60 seconds, from 30 seconds to 2 minutes, from 1 minutes to 3 minutes, or from 2 minutes to 5 minutes).
  • the liquid sample includes from 1 ⁇ 10 5 to 1 ⁇ 10 15 of the one or more analytes per milliliter of the liquid sample (e.g., from 1 ⁇ 10 5 to 1 ⁇ 10 6 , 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 12 , or 1 ⁇ 10 11 to 1 ⁇ 10 15 analytes per milliliter); (ii) the liquid sample includes from 1 ⁇ 10 6 to 1 ⁇ 10 13 of the magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter); (iii) the magnetic particles have a T 2 relaxivity per particle of from 1 ⁇ 10 4 to 1 ⁇
  • the invention features a system for the detection of one or more analytes, the system including: (a) a first unit including (a1) a permanent magnet defining a magnetic field; (a2) a support defining a well for holding a liquid sample including magnetic particles and the one or more analytes and having an RF coil disposed about the well, the RF coil configured to detect a signal by exposing the liquid sample to a bias homogenous magnetic field created using the permanent magnet and an RF pulse sequence; and (a3) one or more electrical elements in communication with the RF coil, the electrical elements configured to amplify, rectify, transmit, and/or digitize the signal; and (b) one or more second units including (b1) a permanent magnet adjacent a first sample position for holding a liquid sample and configured to apply a first gradient magnetic field to the liquid sample.
  • the one or more second units can further include a second permanent magnet adjacent a second sample position for holding a liquid sample and configured to apply a second gradient magnetic field to the liquid sample, the second magnetic field aligned to apply a gradient magnetic field to the sample from a direction different from the direction of the first field gradient, and a means for moving a liquid sample from the first sample position to the second sample position.
  • the one or more second units is incapable of measuring a signal (e.g., incapable of measuring an NMR relaxation rate), and/or lacks an RF coil, or a means for producing an RF pulse.
  • the angle between the first direction and the second direction relative to the liquid sample is between 0° and 180° (e.g., from 0° to 10°, 5° to 120°, 20° to 60°, 30° to 80°, 45° to 90°, 60° to 120°, 80° to 135°, or from 120° to 180°).
  • the system can further include a sample holder for holding the liquid sample and configured to move the liquid sample from the first position to the second position.
  • the system includes an array of the one or more second units for assisting the agglomeration of an array of samples simultaneously.
  • the array can be configured to rotate one or more liquid from a first position in which a magnetic field is applied to the side of a sample to a second position in which a magnetic field is applied to the bottom of a sample.
  • the system can include a cartridge unit, an agitation unit, a centrifuge, or any other system component described herein.
  • the system can further include (c) a third unit including a removable cartridge sized to facilitate insertion into and removal from the system and having a compartment including one or more populations of magnetic particles having binding moieties on their surfaces, wherein the binding moieties are operative to alter an aggregation of the magnetic particles in the presence of the one or more analytes.
  • the removable cartridge is a modular cartridge including (i) a reagent module for holding one or more assay reagents; and (ii) a detection module including a detection chamber for holding a liquid sample including magnetic particles and one or more analytes, wherein the reagent module and the detection module can be assembled into the modular cartridge prior to use, and wherein the detection chamber is removable from the modular cartridge.
  • the modular cartridge can further include an inlet module, wherein the inlet module, the reagent module, and the detection module can be assembled into the modular cartridge prior to use, and wherein the inlet module is sterilizable.
  • the system can further include a system computer with processor for implementing an assay protocol and storing assay data
  • the removable cartridge further includes (i) a readable label indicating the analyte to be detected, (ii) a readable label indicating the assay protocol to be implemented, (iii) a readable label indicating a patient identification number, (iv) a readable label indicating the position of assay reagents contained in the cartridge, or (v) a readable label including instructions for the programmable processor.
  • the invention further features a system for the detection of one or more analytes, the system including: (a) a first unit including (a1) a permanent magnet defining a magnetic field; (a2) a support defining a well for holding a liquid sample including magnetic particles and the one or more analytes and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using the permanent magnet and an RF pulse sequence; and (a3) one or more electrical elements in communication with the RF coil, the electrical elements configured to amplify, rectify, transmit, and/or digitize the signal; and (b) a second unit including a removable cartridge sized to facilitate insertion into and removal from the system, wherein the removable cartridge is a modular cartridge including (i) a reagent module for holding one or more assay reagents; and (ii) a detection module including a detection chamber for holding a liquid sample including the magnetic particles and the one or more analytes, where
  • the modular cartridge can further include an inlet module, wherein the inlet module, the reagent module, and the detection module can be assembled into the modular cartridge prior to use, and wherein the inlet module is sterilizable.
  • the system further includes a system computer with processor for implementing an assay protocol and storing assay data
  • the removable cartridge further includes (i) a readable label indicating the analyte to be detected, (ii) a readable label indicating the assay protocol to be implemented, (iii) a readable label indicating a patient identification number, (iv) a readable label indicating the position of assay reagents contained in the cartridge, or (v) a readable label including instructions for the programmable processor.
  • the system can include a cartridge unit, an agitation unit, a centrifuge, or any other system component described herein.
  • the invention features an agitation unit for the automated mixing of a liquid sample in a sample chamber, including a motor for providing a rotational driving force to a motor shaft coupled to a drive shaft, the driveshaft having a first end coupled to the motor shaft and a second end coupled to a plate bearing a sample holder for holding the sample chamber, the draft shaft including a first axis coaxial to the motor shaft, and a second axis that is offset and parallel to the motor shaft, such that the second axis of the driveshaft, the plate, and the sample holder are driven in an orbital path, wherein the motor includes an index mark and/or other position sensing means such as an optical, magnetic or resistive position encoder for positioning the sample chamber in a predetermined position following the mixing or a sensor which tracks the sample's position throughout its path.
  • a motor for providing a rotational driving force to a motor shaft coupled to a drive shaft
  • the driveshaft having a first end coupled to the motor shaft and a second end coupled to a plate bearing a sample
  • the invention features a system for the detection of one or more analytes, the system including: (a) a first unit including (a1) a permanent magnet defining a magnetic field; (a2) a support defining a well for holding a liquid sample including magnetic particles and the one or more analytes and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using the permanent magnet and an RF pulse sequence; and (a3) one or more electrical elements in communication with the RF coil, the electrical elements configured to amplify, rectify, transmit, and/or digitize the signal; and (b) a second unit for the automated mixing of a liquid sample in a sample chamber, including a motor for providing a rotational driving force to a motor shaft coupled to a drive shaft, the driveshaft having a first end coupled to the motor shaft and a second end coupled to a plate bearing a sample holder for holding the sample chamber, the draft shaft including a first axis coaxial
  • the system further includes a robotic arm for placing the sample chamber in, and removing the sample chamber from, the agitation unit.
  • the invention further features a system for the detection of one or more analytes, the system including: (a) a first unit including (a1) a permanent magnet defining a magnetic field; (a2) a support defining a well for holding a liquid sample including magnetic particles and the one or more analytes and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using the permanent magnet and an RF pulse sequence; and (a3) one or more electrical elements in communication with the RF coil, the electrical elements configured to amplify, rectify, transmit, and/or digitize the signal; and (b) a centrifuge including a motor for providing a rotational driving force to a drive shaft, the drive shaft having a first end coupled to the motor and a second end coupled to a centrifuge rotor bearing a sample holder for holding the sample chamber, wherein the motor includes an index mark and/or other position sensing means such as an optical, magnetic or resistive position encode
  • the invention further features a system for the detection of one or more analytes, the system including: (a) a disposable sample holder defining a well for holding a liquid sample and having an RF coil contained within the disposable sample holder and disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using the permanent magnet and an RF pulse sequence, wherein the disposable sample holder includes one or more fusable links; and (b) an MR reader including (b1) a permanent magnet defining a magnetic field; (b2) an RF pulse sequence and detection coil; (b3) one or more electrical elements in communication with the RF coil, the electrical elements configured to amplify, rectify, transmit, and/or digitize the signal; and (b4) one or more electrical elements in communication with the fusable link and configured to apply excess current to the fusable link, causing the link to break and rendering the coil inoperable following a predetermined working lifetime.
  • the electrical element in communication with the RF coil is
  • the invention features a system for the detection of creatinine, tacrolimus, and Candida , the system including: (a) a first unit including (a1) a permanent magnet defining a magnetic field; (a2) a support defining a well for holding a liquid sample including magnetic particles and the creatinine, tacrolimus, and Candida and having an RF coil disposed about the well, the RF coil configured to detect signal produced by exposing the liquid sample to a bias magnetic field created using the permanent magnet and an RF pulse sequence; and (a3) an electrical element in communication with the RF coil, the electrical element configured to amplify, rectify, transmit, and/or digitize the signal; and (b) a second unit including a removable cartridge sized to facilitate insertion into and removal from the system, wherein the removable cartridge is a modular cartridge including (i) a plurality of reagent modules for holding one or more assay reagents; and (ii) a plurality of detection module including a detection chamber for holding a liquid sample including the magnetic particles and
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 or 80 ⁇ g to 100 ⁇ g) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the liquid sample includes from 1 ⁇ 10 6 to 1 ⁇ 10 13 of the magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter).
  • the invention features a method for measuring the concentration of creatinine in a liquid sample, the method including: (a) contacting a solution with (i) magnetic particles to produce a liquid sample including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the invention features a multivalent binding agent including two or more creatinine moieties covalently linked to a scaffold.
  • the multivalent binding agent is a compound of formula (I): (A) n -(B) (I) wherein (A) is
  • (B) is a polymeric scaffold covalently attached to each (A), m is an integer from 2 to 10, and n is an integer from 2 to 50.
  • the invention features a solution including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the solution (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 600 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, or from 500 to 600 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1 ⁇ 10 8 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or from 1 ⁇ 10 10 to 1
  • n is an integer from 2 to 10.
  • the invention further features solution including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the solution (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 600 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, or from 500 to 600 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1 ⁇ 10 8 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or from 1 ⁇ 10 10 to 1 ⁇
  • (B) is a polymeric scaffold.
  • the invention further features a method for measuring the concentration of tacrolimus in a liquid sample, the method including: (a) contacting a solution with (i) magnetic particles to produce a liquid sample including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the liquid sample (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM
  • the magnetic particles are substantially monodisperse; exhibit nonspecific reversibility in the absence of the analyte and multivalent binding agent; and/or the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran).
  • the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.2% to 0.4%, or from 0.3% to 0.5% nonionic surfactant), or a combination thereof.
  • a buffer from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%,
  • the magnetic particles include a surface decorated with 40 ⁇ g to 100 ⁇ g (e.g., 40 ⁇ g to 60 ⁇ g, 50 ⁇ g to 70 ⁇ g, 60 ⁇ g to 80 ⁇ g, or 80 ⁇ g to 100 ⁇ g,) of one or more proteins per milligram of the magnetic particles.
  • the liquid sample can include a multivalent binding agent bearing a plurality of analytes conjugated to a polymeric scaffold.
  • the invention features a multivalent binding agent including two or more tacrolimus moieties, including tacrolimus metabolites described herein or structurally similar compounds for which the antibody has affinity covalently linked to a scaffold.
  • the multivalent binding agent is a compound of formula (II): (A) n -(B) (II) wherein (A) is
  • (B) is a polymeric scaffold covalently attached to each (A), and n is an integer from 2 to 50.
  • the invention features a solution including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles per milliliter of the solution (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles per milliliter), wherein the magnetic particles have a mean diameter of from 150 nm to 600 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, or from 500 to 600 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1 ⁇ 10 8 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or from 1 ⁇ 10 10 to
  • (B) is a polymeric scaffold.
  • the magnetic particles are substantially monodisperse; (ii) the magnetic particles exhibit nonspecific reversibility in plasma; (iii) the magnetic particles further include a surface decorated with a blocking agent selected from albumin, fish skin gelatin, gamma globulin, lysozyme, casein, peptidase, and an amine-bearing moiety (e.g., amino polyethyleneglycol, glycine, ethylenediamine, or amino dextran); (iv) the liquid sample further includes a buffer, from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/w) albumin), from 0.01% to 0.5% nonionic surfactant (e.g., from 0.01% to 0.05%, 0.05% to 0.1%, 0.05% to 0.2%, 0.1% to 0.3%, 0.
  • a blocking agent selected from albumin, fish
  • the invention features a removable cartridge sized to facilitate insertion into and removal from a system of the invention, wherein the removable cartridge includes one or more chambers for holding a plurality of reagent modules for holding one or more assay reagents, wherein the reagent modules include (i) a chamber for holding from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles) having a mean diameter of from 100 nm to 699 nm (e.g., from 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, or from 500 to 699 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 8 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g.,
  • the invention features a removable cartridge sized to facilitate insertion into and removal from a system of the invention, wherein the removable cartridge comprises one or more chambers for holding a plurality of reagent modules for holding one or more assay reagents, wherein the reagent modules include (i) a chamber for holding from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , or 1 ⁇ 10 10 to 1 ⁇ 10 13 magnetic particles) having a mean diameter of from 700 nm to 1200 nm (e.g., from 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm), a T 2 relaxivity per particle of from 1 ⁇ 10 9 to 1 ⁇ 10 12 mM ⁇ 1 s ⁇ 1 (e.g., from 1
  • the magnetic particles can be any described herein, decorated with any binding moieties described herein, for detecting any analyte described herein.
  • the magnetic particles and buffer are together in a single chamber withing the cartridge.
  • the buffer includes from 0.1% to 3% (w/w) albumin, from 0.01% to 0.5% nonionic surfactant, a lysis agent, or a combination thereof.
  • the removable cartridge can further include a chamber including beads for lysing cells; a chamber including a polymerase; and/or a chamber including a primer.
  • the invention features a removable cartridge sized to facilitate insertion into and removal from a system of the invention, wherein the removable cartridge includes one ore more chambers for holding a plurality of reagent modules for holding one or more assay reagents, wherein the reagent modules include (i) a chamber for holding from 1 ⁇ 10 8 to 1 ⁇ 10 10 magnetic particles having a mean diameter of from 100 nm to 350 nm, a T 2 relaxivity per particle of from 5 ⁇ 10 8 to 1 ⁇ 10 10 and binding moieties on their surfaces (e.g., antibodies, conjugated analyte), the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent; and (ii) a chamber for holding a buffer including from 0.1% to 3% (w/w) albumin (e.g., from 0.1% to 0.5%, 0.3% to 0.7%, 0.5% to 1%, 0.8% to 2%, or from 1.5% to 3% (w/
  • the liquid sample can include from 1 ⁇ 10 8 to 1 ⁇ 10 10 magnetic particles having a mean diameter of from 100 nm to 350 nm, a T 2 relaxivity per particle of from 5 ⁇ 10 8 to 1 ⁇ 10 10 mM ⁇ 1 s ⁇ 1 , and binding moieties on their surfaces (e.g., antibodies, conjugated analyte), the binding moieties operative to alter the specific aggregation of the magnetic particles in the presence of the one or more analytes or a multivalent binding agent.
  • binding moieties on their surfaces e.g., antibodies, conjugated analyte
  • the disruption of the red blood cells can be carried out using an erythrocyte lysis agent (i.e., a lysis buffer, or a nonionic detergent).
  • Erythrocyte lysis buffers which can be used in the methods of the invention include, without limitation, isotonic solutions of ammonium chloride (optionally including carbonate buffer and/or EDTA), and hypotonic solutions.
  • the erythrocyte lysis agent can be an aqueous solutions of nonionic detergents (e.g., nonyl phenoxypolyethoxylethanol (NP-40), 4-octylphenol polyethoxylate (Triton-X100), Brij-58, or related nonionic surfactants, and mixtures thereof).
  • nonionic detergents e.g., nonyl phenoxypolyethoxylethanol (NP-40), 4-octylphenol polyethoxylate (Triton-X100), Brij-58, or related nonionic surfactants, and mixtures thereof.
  • the erythrocyte lysis agent disrupts at least some of the red blood cells, allowing a large fraction of certain components of whole blood (e.g., certain whole blood proteins) to be separated (e.g., as supernatant following centrifugation) from the white blood cells, yeast cells, and/or bacteria cells present in the whole blood sample.
  • the resulting pellet is reconstituted to form an extract
  • the methods, kits, cartridges, and systems of the invention can be configured to detect a predetermined panel of pathogen-associated analytes.
  • the panel can be a candida fungal panel configured to individually detect three or more of Candida guilliermondii, C. albicans, C. glabrata, C. krusei, C. Lusitaniae, C. parapsilosis , and C. tropicalis .
  • the panel can be a bacterial panel configured to individually detect three or more of coagulase negative Staphylococcus, Enterococcus faecalis, E.
  • the panel can be a viral panel configured to individually detect three or more of Cytomegalovirus (CMV), Epstein Barr Virus, BK Virus, Hepatitis B virus, Hepatitis C virus, Herpes simplex virus (HSV), HSV1, HSV2, Respiratory syncytial virus (RSV), Influenza; Influenza A, Influenza A subtype H1, Influenza A subtype H3, Influenza B, Human Herpes Virus 6, Human Herpes Virus 8, Human Metapneumovirus (hMPV), Rhinovirus, Parainfluenza 1, Parainfluenza 2, Parainfluenza 3, and Adenovirus.
  • CMV Cytomegalovirus
  • BK Virus Herpes simplex virus
  • HSV Herpes simplex virus
  • HSV1 HSV2 Herpes simplex virus
  • RSV Respiratory syncytial virus
  • Influenza Influenza
  • Influenza A Influenza A subtype H1, Influenza A subtype H3, Influenza B
  • the panel can be a bacterial panel configured to individually detect three or more of E. coli , CoNS (coagulase negative staph), Pseudomonas aeruginosa, S. aureus, E. faecium, E. faecalis , and Klebsiella pneumonia .
  • the panel can be a bacterial panel configured to individually detect three or more of A. fumigates , and A. flavum .
  • the panel can be a bacterial panel configured to individually detect three or more of Acinetobacter baumannii, Enterobacter aeraogenes, Enterobacter cloacae, Klebsiella oxytoca, Proteus mirabilis, Serratia marcescens, Staphylococcus haemolyticus, Stenotro - phomonas maltophilia, Streptococcus agalactie, Streptococcus mitis, Streptococcus pneumonia , and Streptococcus pyogenes .
  • the panel can be a meningitis panel configured to individually detect three or more of Streptococcus pneumonia, H.
  • the panel can be configured to individually detect three or more of N. gonnorrhoeae, S. aureus, S. pyogenes , CoNS, and Borrelia burgdorferi .
  • the panel can be configured to individually detect three or more of C. Difficile , Toxin A, and Toxin B.
  • the panel can be a pneumonia panel configured to individually detect three or more of Streptococcus pneumonia , MRSA, Legionella, C. pneumonia , and Mycoplasma Pneumonia .
  • the panel can be configured to individually detect three or more of treatment resistant mutations selected from mecA, vanA, vanB, NDM-1, KPC, and VIM.
  • the panel can be configured to individually detect three or more of H. influenza, N. gonnorrhoeae, H. pylori, Campylobacter, Brucella, Legionella , and Stenotrophomonas maltophilia .
  • the panel can be configured to detect total viral load caused by CMV, EBV, BK Virus, HIV, HBV, and HCV.
  • the panel can be configured to detect fungal load and/or bacterial load. Viral load determination can be using a standard curve and measuring the sample against this standard curve or some other method of quantitation of the pathogen in a sample.
  • the quantitative measuring method may include real-time PCR, competitive PCR (ratio of two cometiting signals) or other methods mentioned here.
  • the panel can be configured to detect immune response in a subject by monitoring PCT, MCP-1, CRP, GRO-alpha, High mobility group-box 1 protein (HMBG-1), IL-1 receptor, IL-1 receptor antagonist, IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, macrophage inflammatory protein (MIP-1), macrophage migration inhibitory factor (MIF), osteopontin, RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), Th1, Th17, and/or TNF- ⁇ .
  • MIP-1 macrophage inflammatory protein
  • MIF macrophage migration inhibitory factor
  • osteopontin RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), Th1, Th17, and/or TNF- ⁇ .
  • the panel can be configured to individually detect three or more of Ehrlichea, Mycobacterium, Syphillis, Borrelia burgdorferi, Cryptococcus, Histoplasma , and Blastomyces .
  • the panel can be an influenza panel configured to individually detect three or more of Influenza A, Influenza B, RSV, Parainfluenza, Meta-pneumovirus, Rhinovirus, and Adenovirus.
  • the methods, kits, cartridges, and systems of the invention can be configured to reduce sample to sample variablility by determining a magnetic resonance signal prior to and after hybridization.
  • the addition of derivatized nanoparticles to the sample prior to methods to enhance clustering may provide a baseline, internal T 2 signal that can either be subtracted or used to modify the T 2 signal after analyte-derivatized particle binding and clustering. This method may also be used to determine or manage cartridge to cartridge variability.
  • aggregation means the binding of two or more magnetic particles to one another, e.g., via a multivalent analyte, multimeric form of analyte, antibody, nucleic acid molecule, or other binding molecule or entity.
  • magnetic particle agglomeration is reversible.
  • analyte is meant a substance or a constituent of a sample to be analyzed.
  • exemplary analytes include one or more species of one or more of the following: a protein, a peptide, a polypeptide, an amino acid, a nucleic acid, an oligonucleotide, RNA, DNA, an antibody, a carbohydrate, a polysaccharide, glucose, a lipid, a gas (e.g., oxygen or carbon dioxide), an electrolyte (e.g., sodium, potassium, chloride, bicarbonate, BUN, magnesium, phosphate, calcium, ammonia, lactate), a lipoprotein, cholesterol, a fatty acid, a glycoprotein, a proteoglycan, a lipopolysaccharide, a cell surface marker (e.g., CD3, CD4, CD8, IL2R, or CD35), a cytoplasmic marker (e.g., CD4/CD8 or CD4/viral load),
  • the term “small molecule” refers to a drug, medication, medicament, or other chemically synthesized compound that is contemplated for human therapeutic use.
  • biological refers to a substance derived from a biological source, not synthesized and that is contemplated for human therapeutic use.
  • a “biomarker” is a biological substance that can be used as an indicator of a particular disease state or particular physiological state of an organism, generally a biomarker is a protein or other native compound measured in bodily fluid whose concentration reflects the presence or severity or staging of a disease state or dysfunction, can be used to monitor therapeutic progress of treatment of a disease or disorder or dysfunction, or can be used as a surrogate measure of clinical outcome or progression.
  • the term “metabolic biomarker” refers to a substance, molecule, or compound that is synthesized or biologically derived that is used to determine the status of a patient or subject's liver or kidney function.
  • the term “genotyping” refers to the ability to determine genetic differences in specific genes that may or may not affect the phenotype of the specific gene.
  • the term “phenotype” refers to the resultant biological expression, (metabolic or physiological) of the protein set by the genotype.
  • the term “gene expression profiling” refers to the ability to determine the rate or amount of the production of a gene product or the activity of gene transcription in a specific tissue, in a temporal or spatial manner.
  • proteomic analysis refers to a protein pattern or array to identify key differences in proteins or peptides in normal and diseased tissues. Additional exemplary analytes are described herein.
  • analyte further includes components of a sample that are a direct product of a biochemical means of amplification of the initial target analyte, such as the product of a nucleic acid amplification reaction.
  • an “isolated” nucleic acid molecule is meant a nucleic acid molecule that is removed from the environment in which it naturally occurs.
  • a naturally-occurring nucleic acid molecule present in the genome of cell or as part of a gene bank is not isolated, but the same molecule, separated from the remaining part of the genome, as a result of, e.g., a cloning event, amplification, or enrichment, is “isolated.”
  • an isolated nucleic acid molecule is free from nucleic acid regions (e.g., coding regions) with which it is immediately contiguous, at the 5′ or 3′ ends, in the naturally occurring genome.
  • Such isolated nucleic acid molecules can be part of a vector or a composition and still be isolated, as such a vector or composition is not part of its natural environment.
  • linked means attached or bound by covalent bonds, non-covalent bonds, and/or linked via Van der Waals forces, hydrogen bonds, and/or other intermolecular forces.
  • magnetic particle refers to particles including materials of high positive magnetic susceptibility such as paramagnetic compounds, superparamagnetic compounds, and magnetite, gamma ferric oxide, or metallic iron.
  • nonspecific reversibility refers to the colloidal stability and robustness of magnetic particles against non-specific aggregation in a liquid sample and can be determined by subjecting the particles to the intended assay conditions in the absence of a specific clustering moiety (i.e., an analyte or an agglomerator). For example, nonspecific reversibility can be determined by measuring the T 2 values of a solution of magnetic particles before and after incubation in a uniform magnetic field (defined as ⁇ 5000 ppm) at 0.45 T for 3 minutes at 37° C.
  • a uniform magnetic field defined as ⁇ 5000 ppm
  • Magnetic particles are deemed to have nonspecific reversibility if the difference in T 2 values before and after subjecting the magnetic particles to the intended assay conditions vary by less than 10% (e.g., vary by less than 9%, 8%, 6%, 4%, 3%, 2%, or 1%). If the difference is greater than 10%, then the particles exhibit irreversibility in the buffer, diluents, and matrix tested, and manipulation of particle and matrix properties (e.g., coating and buffer formulation) may be required to produce a system in which the particles have nonspecific reversibility.
  • the test can be applied by measuring the T 2 values of a solution of magnetic particles before and after incubation in a gradient magnetic field 1 Gauss/mm-10000 Gauss/mm.
  • NMR relaxation rate refers to a measuring any of the following in a sample T 1 , T 2 , T 1 /T 2 hybrid, T 1rho , T 2rho , and T 2 *.
  • the systems and methods of the invention are designed to produce an NMR relaxation rate characteristic of whether an analyte is present in the liquid sample. In some instances the NMR relaxation rate is characteristic of the quantity of analyte present in the liquid sample.
  • T 1 /T 2 hybrid refers to any detection method that combines a T 1 and a T 2 measurement.
  • the value of a T 1 /T 2 hybrid can be a composite signal obtained through the combination of, ratio, or difference between two or more different T 1 and T 2 measurements.
  • the T 1 /T 2 hybrid can be obtained, for example, by using a pulse sequence in which T 1 and T 2 are alternatively measured or acquired in an interleaved fashion.
  • the T 1 /T 2 hybrid signal can be acquired with a pulse sequence that measures a relaxation rate that is comprised of both T 1 and T 2 relaxation rates or mechanisms.
  • pathogen means an agent causing disease or illness to its host, such as an organism or infectious particle, capable of producing a disease in another organism, and includes but is not limited to bacteria, viruses, protozoa, prions, yeast and fungi or pathogen by-products.
  • Pathogen by-products are those biological substances arising from the pathogen that can be deleterious to the host or stimulate an excessive host immune response, for example pathogen antigen/s, metabolic substances, enzymes, biological substances, or toxins.
  • pathogen-associated analyte an analyte characteristic of the presence of a pathogen (e.g., a bacterium, fungus, or virus) in a sample.
  • the pathogen-associated analyte can be a particular substance derived from a pathogen (e.g., a protein, nucleic acid, lipid, polysaccharide, or any other material produced by a pathogen) or a mixture derived from a pathogen (e.g., whole cells, or whole viruses).
  • the pathogen-associated analyte is selected to be characteristic of the genus, species, or specific strain of pathogen being detected.
  • the pathogen-associated analyte is selected to ascertain a property of the pathogen, such as resistance to a particular therapy.
  • the pathogen-associated analyte can be a gene, such as a Van A gene or Van B gene, characteristic of vancomycin resistance in a number of different bacterial species.
  • pulse sequence or “RF pulse sequence” is meant one or more radio frequency pulses to be applied to a sample and designed to measure, e.g., certain NMR relaxation rates, such as spin echo sequences.
  • a pulse sequence may also include the acquisition of a signal following one or more pulses to minimize noise and improve accuracy in the resulting signal value.
  • signal refers to an NMR relaxation rate, frequency shift, susceptibility measurement, diffusion measurement, or correlation measurements.
  • size of a magnetic particle refers to the average diameter for a mixture of the magnetic particles as determined by microscopy, light scattering, or other methods.
  • substantially monodisperse refers to a mixture of magnetic particles having a polydispersity in size distribution as determined by the shape of the distribution curve of particle size in light scattering measurements.
  • the FWHM (full width half max) of the particle distribution curve less than 25% of the peak position is considered substantially monodisperse.
  • only one peak should be observed in the light scattering experiments and the peak position should be within one standard deviation of a population of known monodisperse particles.
  • T 2 relaxivity per particle is meant the average T 2 relaxivity per particle in a population of magnetic particles.
  • unfractionated refers to an assay in which none of the components of the sample being tested are removed following the addition of magnetic particles to the sample and prior to the NMR relaxation measurement.
  • FIG. 1A is a schematic diagram of an NMR unit for detection of a signal response of a sample to an RF pulse sequence, according to an illustrative embodiment of the invention.
  • FIG. 1B depicts a typical coil configuration surrounding a sample tube for measuring a relaxation signal in a 20 ⁇ l sample.
  • FIGS. 2A-2E illustrate micro coil geometries which can be used in NMR (for excitation and/or detection); designs include, but are not limited to a wound solenoid coil ( FIG. 2A ), a planar coil ( FIG. 2B ), a MEMS solenoid coil ( FIG. 2C ), a MEMS Helmholz coil ( FIG. 2D ), and a saddle coil ( FIG. 2E ), according to an illustrative embodiment of the invention.
  • Three dimensional lithographic coil fabrication of well characterized coils used in MR detection is also established and can be used for these applications, Demas et al. “Electronic characterization of lithographically patterned microcoils for high sensitivity NMR detection” J Magn Reson 200:56 (2009).
  • FIG. 3 is a drawing depicting an aggregation assay of the invention.
  • the magnetic particles (dots) are coated with a binding agent (i.e., antibody, oligo, etc.) such that in the presence of analyte, or multivalent binding agent, aggregates are formed.
  • the dotted circles represent the diffusion sphere or portion of the total fluid volume that a solution molecule may experience via its diffusion during a T 2 measurement (the exact path traveled by a water molecule is random, and this drawing is not to scale).
  • Aggregation (right hand side) depletes portions of the sample from the microscopic magnetic non-uniformities that disrupt the water's T 2 signal, leading to an increase in T 2 relaxation.
  • FIGS. 4A-4E are a series of graphs depicting the dependence of transverse relaxivity (R 2 ) ( FIG. 4A ) or T2 ( FIGS. 4B-4E ) on particle diameter and particle aggregation.
  • FIG. 4A is a graph depicting the motional averaging regime (light line, left side); the R 2 (1/T 2 ) measured by a CPMG sequence increases as particle size increases because the refocusing pulses are ineffective to counteract the dephasing effects of the particles.
  • the visit limited regime dark line, right side
  • the refocusing pulses begin to become effective and the R 2 decreases as particle size increases.
  • the R 2 * in the motional averaging regime matches the R 2 and the R 2 * reaches a constant value in the visit limited regime.
  • the system is in the static dephasing regime.
  • FIG. 4B is a graph depicting the same light and dark curves plotted in terms of T 2 and diameter, on a linear scale.
  • the black dashed line represents the T 2 * measured in a non-uniform magnetic field where T 2 * is always lower than T 2 and doesn't reflect the particle size.
  • the data points are the same as well.
  • FIG. 4C is a graph depicting the monodisperse clustering model and showing that T 2 will follow the curve as analyte is added because the average diameter of the population particles will cover all intermediate diameters between the initial and final states.
  • FIG. 4D is a graph depicting the polydisperse model and showing that the T 2 will transition between the two points on this curve when particles form clusters of specific sizes.
  • the response curve will be linear with regard to analyte addition, but non-linear with regard to volume fraction of clusters, because particles transition between state 1 and state 2.
  • the slope of the response curve is directly proportional to the sensitivity of the assay.
  • 4E is a graph showing the two regimes for particle aggregation and T 2 affects based on particle size and how clustering assays in the different regimes map onto the T 2 versus diameter curves (i) for the motional averaging regime T 2 decreases when particles cluster; and (ii) for the slow motion regime T 2 increases when particles cluster.
  • the boundary between the two regimes is ca. 100 nm diameter particles.
  • FIGS. 5A-5C are drawings depicting different assay formats for the assays of the invention.
  • FIG. 5A depicts an agglomerative sandwich immunoassay in which two populations of magnetic particles are designed to bind to two different epitopes of an analyte.
  • FIG. 5B depicts a competitive immunoassay in which analyte in a liquid sample binds to a multivalent binding agent (a multivalent antibody), thereby inhibiting aggregation.
  • FIG. 5C depicts a hybridization-mediated agglomerative assay in which two populations of particles are designed to bind to the first and second portions of a nucleic acid target, respectively.
  • FIG. 6 illustrates a modular cartridge concept in sections that can be packaged and stored separately. This is done, for example, so that the inlet module (shown elevated with inverted Vacutainer tube attached) can be sterilized while the reagent holding module in the middle is not. This allows the component containing reagents to be the only refrigerated component.
  • FIGS. 7A-7F depict a Vacutainer inlet module.
  • FIG. 7A shows it in the inverted position after the user has removed the closure from the Vacutainer tube and placed the cartridge onto it.
  • FIG. 7B shows the molded in path that the blood will follow out of the Vacutainer and into the sample loading region once the cartridge is turned right side up.
  • the foil seal can be the bottom side of the channels, forming an inexpensively molded part with closed channels.
  • FIG. 7C is a cutaway view showing the vent tube which allows air to enter into the vial as the blood leaves and fills the sample region.
  • FIGS. 7D-7F depict an inlet module for sample aliquoting designed to interface with uncapped vacutainer tubes, and to aliquot two a sample volume that can be used to perform, for example, a candida assay.
  • the inlet module has two hard plastic parts, that get ultrasonically welded together and foil sealed to form a network of channels to allow a flow path to form into the first well overflow to the second sample well.
  • a soft vacutainer seal part is used to for a seal with the vacutainer. It has a port for sample flow, and a venting port, to allow the flow to occur.
  • FIG. 8 depicts the sample inlet module with the foil seal removed. On the top, one can see the small air inlet port to the left, the larger sample well in the center and a port which connects them together. This port provides a channel through which air can flow once the foil seal is pierced. It also provides an overflow into the body of the module to allow excess blood to drain away and not spill over. This effectively meters the blood sample to the volume contained in the sample well.
  • FIGS. 9A-9C depict a reagent module.
  • FIG. 9A depicts the module of the cartridge that is intended to hold reagents and consumables for use during the assay. On the left are sealed pre-dispensed aliquots of reagents. On the right is a 2.8 ml conical bottomed centrifuge tube that is used for initial centrifugation of the blood. The other holes can be filled as need with vials, microcentrifuge tubes, and pipette tips.
  • FIG. 9B is a cutaway view of the reagent module showing the holders for the pre-aliquoted reagent tips, including the feature at the bottom into which the tips are pressed to provide a seal.
  • FIG. 9 C depicts three representative pipette tips into which reagents can be pre-dispensed, and then the backs sealed. The tips are pressed into the sample holder to provide a seal.
  • FIGS. 10A and 10B depict an alternative design of the modular cartridge, showing a detection module with a recessed well for use in assays that require PCR.
  • Cross-contamination from PCR products is controlled in two ways.
  • the seals that are on the detection tubes are designed to seal to a pipette tip as it penetrates.
  • the instrument provides air flow through the recessed well by means of holes in the well to ensure that any aerosol is carried down and does not travel throughout the machine.
  • FIG. 11 depicts a detection module of cartridge showing detection tubes and one of the holes used to ensure air flow down and over the tubes during pipetting to help prevent aerosol escape.
  • FIG. 12 depicts a bottom view of the detection module, showing the bottom of the detection tubes and the two holes used to ensure airflow.
  • An optional filter can be inserted here to capture any liquid aerosol and prevent it from entering the machine.
  • This filter could also be a sheet of a hydrophobic material like Gore-tex that will allow air but not liquids to escape.
  • FIGS. 13A-13C depict a detection tube.
  • FIG. 13A is a view of the detection tube.
  • the tube itself could be an off the shelf 200 microliter PCR tube, while the cap is a custom molded elastomer part that provides a pressure resistant duckbill seal on the inside and a first seal to the pipette tip from the top. The seal is thus a make-break type of seal, where one seal is made before the other is broken.
  • FIG. 13B depicts the custom molded seal component. Note the circular hole into which the pipette tip is inserted and the duckbill seal below, which provides a second seal that resists pressure developed in the tube.
  • FIG. 13C depicts the seal showing the duckbill at bottom and the hole at top.
  • FIGS. 14A-14C depict a cartridge for performing a multiplexed assay.
  • FIG. 14A shows a reagent strip for the cartridge.
  • the oval holes are the supports for the detection modules, and these are constructed separately and then placed into the holes.
  • the detection wells could be custom designed or commercially available.
  • FIG. 14B shows the detection module for the cartridge depicted in FIG. 14A .
  • the detection module contains two detection chambers, but could contain any number of chambers as required by the assay and as the detection system (the MR reader) is designed to accept.
  • FIG. 14C depicts an alternate footprint for the modular multiplexed cartridge.
  • This cartridge includes 3 detection modules that are molded as part of the reagent strip, and these portions are popped out of the frame and individually processed at other units (i.e., the NMR unit and/or magnetic assisted agglomeration (MAA) unit) within the assay system.
  • the NMR unit and/or magnetic assisted agglomeration (MAA) unit within the assay system.
  • FIG. 15 is a scheme depicting one embodiment of the cycling gradient magnetic assisted agglomeration (gMAA) method of the invention.
  • Two magnets are placed in two positions such that if the sample tube is placed close to the a region of strong magnetic field gradient produced by the first magnet, the magnetic particles will be drawn towards the direction of the field gradient produced by the first magnet, the sample tube is then placed next to the second magnet producing a field gradient, and the magnetic particles are drawn to the direction of the field gradient produced by second magnet.
  • the cycle can be repeated until the aggregation reaction reaches a steady state (as observed by the change in the NMR relaxation rate of the sample); a smaller number of cycles can be used as well.
  • a single magnet used to produce a field gradient can also be used, while for cycling the sample tube can be moved relative to the magnetic field gradient.
  • FIG. 16 is a scheme depicting a homogenous magnetic assisted agglomeration (hMAA) setup.
  • hMAA homogenous magnetic assisted agglomeration
  • the magnetic particles are shown as dots in a partially clustered state.
  • clustering of the magnetic particles is promoted as the magnetic particles form chains along the direction of the field produced by the hMAA setup.
  • the two magnets are represented by bars, to depict the formation of a standard dipole field.
  • hMAA can also be used to evaluate the nonspecific reversibility of a magnetic particle to assess its utility in an assay of the invention.
  • FIG. 17 depicts a gradient MAA unit configured to apply a gradient magnetic field to the side and to the bottom of a sample.
  • the specific setup has magnets with a surface field of approximately 0.7 T, while the produced gradient is in the order of 0.25 T/mm. Similar gMAA units, covering a much bigger range of fields and gradients can be used.
  • FIGS. 18A-18C depict a gradient MAA unit configured to apply a gradient magnetic field to the side and to the bottom of an array of samples.
  • FIG. 18A depicts the gMAA unit array of 32 bottom magnets and 40 side magnets (32 functional, 8 used to balance the stray magnetic fields seen by all sample), each with a field strength of about 0.5 T, used for assisting agglomeration in an array of samples simultaneously.
  • FIGS. 18B-18C depict a top view ( FIG. 18B ) and side view ( FIG.
  • a setup for the automation of the an automated gMAA unit wherein a plate gMAA along with a configuration for containing an array of samples is cycled between the bottom and side magnet positions by a robotic systems, within a temperature controlled array.
  • the magnets are stationary, while the plate holding the sample tubes moves through a preset trajectory.
  • An exemplary field strength on the surface of individual magnets is 0.4-0.5 T, with a gradient in the order of 0.1 T/mm.
  • FIGS. 19A-19B depict a top view ( FIG. 19A ) and side view ( FIG. 19B ) of a homogenous MAA unit configured to apply a homogenous magnetic field to an array samples.
  • Field strengths from 0.2-0.7 T can be used with homogeneity from 500 to 5000 ppm over the sample tube region.
  • FIG. 20 is a drawing of a vortexer which includes the following components: (i) a sample support, (ii) a main plate, (iii) four linkages, (iv) linear rail and carriage system ( ⁇ 2), (v) a support for driveshaft and rails, (vi) coupling and driveshaft, (vii) a mounting plate, and (viii) a drive motor.
  • FIG. 21 is a drawing of a compact vortexer which includes the following components: (i) a sample support, (ii) a main plate, (iii) two linkages, (iv) linear rail and carriage system, (v) a support for linear rail, (vi) support for driveshaft, (vii) coupling and driveshaft, (viii) a mounting plate, and (ix) a drive motor.
  • FIGS. 22A and 22B depict portions of a vortexer.
  • FIG. 22A is a drawing depicting the bottom portion (i.e., the drive motor, coupling, and drive shaft) of a vortexer of the invention.
  • the motor includes an index mark and/or other position sensing means such as an optical, magnetic or resistive position encoder that allows the motor to find a specific point in its rotation. These index marks are used to home the system, and ensure that the sample can be returned to a known position after mixing and allows the vortexer to be easily accessed by robotic actuators, and thus integrated into an automated system. In lieu of index marks, external home switches or position tracking sensors could be employed.
  • FIG. 22B is a drawing depicting the guide mechanism of a vortexer of the invention.
  • the main plate is connected to the offset axis of the drive shaft and is free to rotate. The plate follows the orbital path around and dictated by the motor shaft.
  • FIGS. 23A-23C are a series of drawings depicting a vortexer utilizing a planetary belt drive.
  • FIG. 23A is an overall view showing the vortexer configured for one large tube.
  • FIG. 23B is a section view showing two tube holders for small tubes.
  • FIG. 23C is an overall view of vortexer showing four tubes and a close up of planetary belt drive mechanism.
  • FIG. 24 is a drawing depicting the components of the creatinine competitive assay of Example 6.
  • a magnetic particle decorated with creatinine is used in combination with a creatinine antibody to form an aggregating system.
  • the creatinine present in a liquid sample competes with the magnetic particles for the antibody, leading to a reduction in aggregation with increasing creatinine concentration.
  • the change in aggregation is observed as a change in the T 2 relaxation rate of the hydrogen nuclei in the water molecules of the liquid sample.
  • the concentration of creatinine is determined.
  • FIGS. 25A-25C are a series of graphs showing the response curve for creatinine competitive assays.
  • FIG. 25A is a graph showing a standard curve for the creatinine competitive assay of Example 6 correlating the observed T 2 relaxation rate with the concentration of creatinine in the liquid sample.
  • FIG. 25B shows the T 2 response of a creatinine-decorated particle with 2 different preparations of antibody. Preparation 1 is pre-production (with aggregated antibody) and Preparation 2 is production purified (no aggregated antibody present).
  • FIG. 25C shows the T 2 response of a creatinine-decorated particle with unaggregated antibody, biotinylated antibody and deliberately multimerized antibody, and confirms the increased clustering ability of multi-valent agglomerating agents.
  • FIG. 26 is a graph showing the specific clustering achieved, as determined via T 2 relaxation rates, with various methods of gMAA as described in Example 10.
  • control is gMAA (magnet exposure+vortex, repeat) in which the relative position of the sample and the magnetic field direction are unchanged with each cycle
  • twist is gMAA (magnet exposure+rotation within magnet, repeat) with rotating tube ca. 90° relative to the gradient magnet with each cycle
  • 180° turn is gMAA (magnet exposure+remove tube from magnet, rotate, place back in magnet, repeat) with rotating tube ca.
  • FIG. 27 is a graph showing the response curve for the creatinine competitive assay for samples processed with alternating side-bottom magnet gMAA as described in Example 11.
  • FIG. 28 is a drawing depicting the tacrolimus competitive assay architecture of Example 9.
  • FIG. 29 is a graph showing a standard curve for the tacrolimus competitive assay of Example 9 correlating the observed T 2 relaxation rate observed for a liquid sample with the concentration of tacrolimus in the liquid sample.
  • FIGS. 30A-30B are graphs depicting the degree to which gMAA assisted aggregation is dependent upon temperature and dwell time in the assay of Example 11.
  • FIG. 30A is a graph showing that the degree of aggregation as determined by measuring the T 2 response of the sample is increased with increasing dwell time at room temperature.
  • FIG. 30B is a graph showing that the degree of aggregation as determined by measuring the T 2 response of the sample is increased with increasing gMAA dwell time at 37° C.
  • increasing temperature and increasing dwell time enhance the extent of gMAA assisted aggregation as observed by changes in the observed T 2 .
  • FIG. 31 is a graph showing that the degree of aggregation as determined by measuring the T 2 response of the sample is increased with increasing the number of gMAA cycles in the assay of Example 13.
  • FIG. 32 is a drawing depicting the Candida agglomerative sandwich assay architecture of Example 14.
  • FIG. 33 is a graph depicting a creatinine inhibition curve (see Example 7) for using an antibody coated particle and an amino-dextran-creatinine multivalent binding agent to induce clustering by competing with any target analyte (creatinine) present in the sample to cause particle clustering.
  • the binding agent used is a 40 kDa dextran with ⁇ 10 creatinines per dextran molecule.
  • FIG. 34 is a graph depicting the evaluation of Tac-dextran conjugates for clustering ability (see Example 8) by performing a titration. As observed, that increased molecular weight of Tac-dextran results in the improved T 2 signal.
  • FIG. 35 is a graph depicting the evaluation of Tac-dextran conjugates for clustering ability (see Example 8) by performing a titration. As observed, higher substitution improved T 2 signal.
  • FIG. 36 is a graph depicting the evaluation of Tac-BSA conjugates for clustering ability (see Example 8) by performing a titration similar to that used for the Tac-dextran conjugates. As observed, clustering performance varies with the tacrolimus substitution ratio.
  • FIG. 37 is a graph depicting the results of T 2 assays for detecting anti-biotin antibody using prepared magnetic particles in blood and PBS matrices as described in Example 1.
  • FIG. 38 is a graph depicting results of T 2 assays for detecting anti-biotin antibody using prepared magnetic particles with (open circle) and without (filled circle) a protein block as described in Examples 8 and 9.
  • FIG. 39 is a graph depicting results of T 2 assays for detecting anti-biotin antibody using prepared magnetic particles having a BSA block (dark filled diamond, square, triangle) or an FSG block (light gray X's and circle) as described in Example 2.
  • FIGS. 40A-40B are schematics of provided particle coatings.
  • FIGS. 41A-41B depict results of T 2 assays for detecting biotin in a competitive assay format described in Example 4.
  • FIG. 41A depicts experimental results in buffer; while FIG. 41B depicts experimental results in lysed blood.
  • FIG. 42 is a sketch of a system of the invention including an NMR unit, a robotic arm, a hMAA unit, a gMAA unit, two agitation units, a centrifuge, and a plurality of heating blocks.
  • FIGS. 43A-43D are images depicting various fluid transfer units which can be used in the systems of the invention.
  • FIGS. 44A and 44B are sketches showing how a system of the invention can be designed to regulate the temperature of the working space.
  • FIGS. 45A and 45B are sketches depicting an NMR unit having a separate casing for regulation of the temperature at the site of the NMR measurement, and useful where tight temperature control is needed for precision of the measurement.
  • the temperature control configuration depicted in this figure is one of many different ways to control temperature.
  • FIGS. 46A is a table and 46 B is a graph depicting the repeatability of Candida measurements by methods of the invention over a period of eight days.
  • FIG. 47 is a scheme describing the work flow for detection of a bacterial or fungal pathogen in a whole blood sample (see Examples 14 and 17).
  • FIGS. 48A and 48B are graphs depicting results from donor samples.
  • FIG. 49 is a dot diagram showing the T2 values measured for five C. albicans clinical isolates spiked into 400 ⁇ L whole blood at concentrations spanning 0 to 1E4 cells/mL. The plotted results are the mean+/ ⁇ 1 SD. The data indicates despite the scatter of absolute T2 values obtained among the different isolates, at 50 cells/mL all values are above that of the no Candida control (3 replicate measurements from 20 independent assays, total of 60 different clustering reactions).
  • FIGS. 50A and 50B are ROC plots of T2 results generated at 10 cells/mL ( FIG. 50A ) and 50 cells/mL ( FIG. 50B ).
  • the area under the curve is often used to quantify the diagnostic accuracy; in this case our ability to discriminate between a Candidemic patient with an infection of 10 cells/mL or 50 cells/mL versus a patient with no Candidemia.
  • the area under the curve is 0.72 which means that if the T2 assay was run on a randomly chosen person with Candidemia at a level of infection of 10 cells/mL, there is an 72% chance their T2 value would be higher than a person with no Candidemia.
  • the clinical accuracy of the test is much higher at 50 cells/mL with the area under the curve at 0.98. Again indicating that in a person with Candidemia at this level of infection, the T2 assay would give a value higher than a sample from a patient without Candidemia 98% of the time. See Example 17.
  • FIG. 51 is a graph depicting the sensitivity of the assay using the standard thermocycle ( ⁇ 3 hours turnaround time) and a process that combines the annealing/elongation steps ( ⁇ 2 hours, 13 minutes turnaround time). Combining the annealing and elongation step in the thermocycling reduces the total assay TAT to 2.25 hours without compromising assay sensitivity.
  • FIG. 52 is a graph depicting the change in T 2 signal with PCR cycling (see Example 18). The results demonstrate that the methods and systems of the invention can be used to perform real time PCR and provide quantitative information about the amount of target nucleic acid present in a sample.
  • FIG. 53 is a series of photographs showing a simple magnetic separator/PCR block insert.
  • FIG. 54 is an image showing the quantity of DNA generated by amplification of (1) 100 copies of genomic C. albicans amplified in the presence of 3′ and 5′ C. albicans single probe nanoparticles; particles were held on the side wall during PCR via magnetic field, (2) 100 copies of genomic C. albicans amplified without nanoparticles, and (3) 100 copies of genomic C. albicans amplified in the presence of 3′ and 5′ C. albicans single probe nanoparticles; no magnetic field.
  • FIGS. 55A-55E are schematic views of a sample tube containing an immobilized portion of magnetizable metal foam (shaded), magnetic particles (circles), and analyte (triangles).
  • a magnetizable metal foam e.g., made of nickel, may be inserted into a conduit and immobilized by exposure to heat, which shrinks the conduit around the metal foam, resulting in a tight seal.
  • a sample containing magnetic particles and analytes is then introduced at one end of the conduit ( FIG. 55A ).
  • the conduit is exposed to a magnet ( FIG. 55B ), and the magnetic particles are attracted to the metal foam and become magnetically trapped within its pores, or crevices.
  • the average diameter of the pores in the metal foam is, e.g., between 100-1000 microns.
  • Analyte molecules can be carried to the metal foam via binding to a magnetic particle, or the fluid can be forced through the metal foam to reach trapped magnetic particles. While trapped in the metal foam, the magnetic particles have enhanced interactions, as they are now confined and are closer to other magnetic particles, and cluster formation is enhanced.
  • the metal foam is then demagnetized ( FIG. 55C ), i.e., the magnetic field of the metal foam becomes negligible.
  • the magnetic particles and analyte cluster complexes largely remain in the metal foam, as the diffusion of magnetic particle clusters is relatively low, although some natural diffusion of the analyte in to and out of the metal foam occurs ( FIG. 55D ).
  • the magnetizable metal foam (hollow cylinder) is free floating in the sample tube with the magnetic particles (circles), and analyte (stars).
  • the magnetization and demagnetization of the free floating metal foam is used to increase the rate of aggregate formation.
  • FIG. 56A depicts a rotary gMAA configuration.
  • the Rotary gMAA can include three configurations for varying magnetic field exposures—side-bottom; side-null and bottom-null (see Example 21).
  • FIG. 56B is a graph comparing T2 signal as a function of various rotary gMAA configurations for varying magnetic field exposures to a sample at a given agglomerator concentration.
  • the rotary side-bottom configuration provided the highest T2 signal at a given agglomerator concentration, followed by the comparison side-bottom plate configuration.
  • Rotary side-null provides equivalent signal to the plate side-bottom; and the bottom-null produces the lowest signal (see Example 21).
  • the invention features systems, devices, and methods for the rapid detection of analytes or determination of analyte concentration in a sample.
  • the systems and methods of the invention employ magnetic particles, an NMR unit, optionally one or more MAA units, optionally one or more incubation stations at different temperatures, optionally one or more vortexer, optionally one or more centrifuges, optionally a fluidic manipulation station, optionally a robotic system, and optionally one or more modular cartridges.
  • the systems, devices, and methods of the invention can be used to assay a biological sample (e.g., blood, sweat, tears, urine, saliva, semen, serum, plasma, cerebrospinal fluid (CSF), feces, vaginal fluid or tissue, sputum, nasopharyngeal aspirate or swab, lacrimal fluid, mucous, or epithelial swab (buccal swab), tissues, organs, bones, teeth, or tumors, among others).
  • a biological sample e.g., blood, sweat, tears, urine, saliva, semen, serum, plasma, cerebrospinal fluid (CSF), feces, vaginal fluid or tissue, sputum, nasopharyngeal aspirate or swab, lacrimal fluid, mucous, or epithelial swab (buccal swab), tissues, organs, bones, teeth, or tumors, among others).
  • the systems, devices, and methods of the invention are used to monitor an environmental condition (e.g., plant growth hormone, insecticides, man-made or environmental toxins, nucleic acid sequences that are important for insect resistance/susceptibility, algae and algae by-products), as part of a bioremediation program, for use in farming plants or animals, or to identify environmental hazards.
  • an environmental condition e.g., plant growth hormone, insecticides, man-made or environmental toxins, nucleic acid sequences that are important for insect resistance/susceptibility, algae and algae by-products
  • biowarfare or biological warfare agents such as ricin, Salmonella typhimurium , botulinum toxin, aflatoxin, mycotoxins, Francisella tularesis , small pox, anthrax, or others.
  • the magnetic particles can be coated with a binding moiety (i.e., antibody, oligo, etc.) such that in the presence of analyte, or multivalent binding agent, aggregates are formed. Aggregation depletes portions of the sample from the microscopic magnetic non-uniformities that disrupt the solvent's T 2 signal, leading to an increase in T 2 relaxation (see FIG. 3 ).
  • a binding moiety i.e., antibody, oligo, etc.
  • the T 2 measurement is a single measure of all spins in the ensemble, measurements lasting typically 1-10 seconds, which allows the solvent to travel hundreds of microns, a long distance relative to the microscopic non-uniformities in the liquid sample.
  • Each solvent molecule samples a volume in the liquid sample and the T 2 signal is an average (net total signal) of all (nuclear spins) on solvent molecules in the sample; in other words, the T 2 measurement is a net measurement of the entire environment experienced by a solvent molecule, and is an average measurement of all microscopic non-uniformities in the sample.
  • the observed T 2 relaxation rate for the solvent molecules in the liquid sample is dominated by the magnetic particles, which in the presence of a magnetic field form high magnetic dipole moments.
  • T 2 (water) ⁇ 2000 ms
  • the observed T 2 value depends upon the particle concentration in a non-linear fashion, and on the relaxivity per particle parameter.
  • the number of magnetic particles, and if present the number of agglomerant particles, remain constant during the assay.
  • the spatial distribution of the particles change when the particles cluster. Aggregation changes the average “experience” of a solvent molecule because particle localization into clusters is promoted rather than more even particle distributions.
  • many solvent molecules do not experience microscopic non-uniformities created by magnetic particles and the T 2 approaches that of solvent.
  • the observed T 2 is the average of the non-uniform suspension of aggregated and single (unaggregated) magnetic particles.
  • the assays of the invention are designed to maximize the change in T 2 with aggregation to increase the sensitivity of the assay to the presence of analytes, and to differences in analyte concentration.
  • Superparamagnetic particles are typically divided into categories of strongly magnetized and weakly magnetized particles, based on the relative magnitude of the precession frequency difference between nuclei at the surface of the particle and nuclei distant from the particle, Aw, and the inter-echo delay of the CPMG detection sequence, ⁇ CP .
  • ⁇ is essentially a relative measure of the effect of the dipolar magnetic field generated by a superparamagnetic particle on the resonant frequency of hydrogen nuclei in adjacent water molecules.
  • ⁇ CP is no shorter than tens of microseconds, so ⁇ must be less than 10 5 for the particles to be within the weakly magnetized regime.
  • Most superparamagnetic particles used for MRSw assays have a surface dephasing ⁇ of approximately 1 ⁇ 10 7 , therefore they are classified as strongly magnetized. This means that the inter-echo delay is always longer than the amount of dephasing that occurs at the surface of a particle.
  • ⁇ D diffusion time, or travel time, of water ( ⁇ D ) relative to the inter-echo time of the pulse sequence, ⁇ CP .
  • Particle solutions are in the long echo limit when the m is significantly less than that ⁇ CP .
  • ⁇ D can be determined by the relationship:
  • ⁇ D R 2 D , ( 1 )
  • ⁇ D is the time it takes a water molecule to diffuse the distance of a particle radius, R, and D the diffusion constant of water, 10 ⁇ 9 m 2 /s.
  • ⁇ D can be thought of as the time it takes a water molecule to pass a hemisphere of a particle, or a flyby time.
  • ⁇ D is much larger than ⁇ CP , then the particle system is within the “short echo limit”.
  • Typical CPMG sequences have echo times on the order of hundreds of microseconds to several milliseconds. Therefore, the “short echo limit” cannot be approached unless the particle diameter approaches 1000 nm.
  • the most common MRSw biosensors are within the “long echo limit” because the length of the inter-echo delays ( ⁇ CP >0.25 ms) is longer than the time it takes a water molecule to diffuse past the hemisphere of a particle (0.2-100 microseconds).
  • the system is in the motional averaging regime; if ⁇ D >1, then the system is in the visit limited regime (also termed the slow motion regime).
  • the refocusing echos in the CPMG pulse sequence cannot efficiently refocus the magnetization that has been dephased by the particles, hence the increase in R 2 (or decrease in T 2 ).
  • the refocusing pulses cannot compensate for increased dephasing by larger particles.
  • the flat region of the static dephasing regime is due to the R 2 being limited by R 2 *.
  • the decreasing R 2 with increasing diameter in the visit limited regime results in the refocusing pulses being able to refocus the dephasing caused by the particles.
  • the R 2 in the slow motion regime exhibits a dependence on the inter-echo delay of the spin echo sequence.
  • the two values are identical in the motional averaging or static dephasing regime and they are different in the visit limited regime.
  • the T 2 * is dominated by the field gradient.
  • the measured T 2 * value is not indicative of the particle or particle cluster size state ( FIG. 4B ).
  • the shape of the R, response as particles agglomerated generally matches the expected trend for the increase in average particle size. The similarity between the R 2 of particle agglomerates and that of spherical particles suggests that one can equate particle aggregates and spherical shapes.
  • the shape of the particle aggregates observed by the magnetic resonance measurement is determined by the ensemble of diffusing water molecules in solution, which can be approximated by the radius of hydration measured by light scattering.
  • the analytical models for R 2 can be applied to magnetic relaxation biosensors to aid in the design of biosensor assays. Conveniently, these models accurately predict the dependence of R 2 on parameters that a biosensor designer can control—iron concentration, temperature, magnetic susceptibility, and particle size. Additionally, these analytical models allow for predictive modeling of the dependence of T 2 relaxation on these parameters. Results are not entirely quantitative, but the general trends and response curves predicted by these models can be instructive.
  • One useful model is the chemical exchange model for strongly magnetized spheres:
  • Equation 2 A modification of Equation 2 can be used to generate a plot that is more intuitive to an assay developer. This plot is in terms of T 2 and particle diameter with linear units rather than logarithmic units ( FIG. 2 ).
  • T 2 magnetic relaxation biosensor assays function due to a transition between dispersed and clustered states.
  • the measured T 2 can follow one of two pathways over the course of an analyte titration.
  • the population of dispersed particles can cluster in a uniform manner leading to an increase in average particle size that is proportional to the amount of analyte that has been added.
  • This type of agglomeration is termed the monodisperse model because it would lead to a monodisperse intermediate population of particles.
  • T 2 would be expected to decrease as particle size increases as long as the system is within the motional averaging regime. As the system approaches and enters the visit limited regime the T 2 would increase with particle size ( FIG. 4C ).
  • a different type of agglomeration that may occur is one in which the addition of analyte seeds the self-assembly of clusters, a process with energetics similar to crystal formation or fractal aggregation.
  • this model one would expect a preferred size for particle clusters that depended on the conditions of the solution. Systems that followed this model would exhibit polydisperse intermediate populations; one would find a mixture of particles with discrete sizes. Given two discrete populations, dispersed particles and clustered particles, the system would transition between the T 2 value of the starting monodisperse population of unclustered particles and the final T 2 value of the fully clustered particles. For both models, full titration may lead to a monodisperse solution of clustered particles.
  • the boundary is typically ca. 100 nm diameter particles.
  • the particle count for 250 nm sized magnetic particles can be ca. 1 ⁇ 10 7 particles, whereas for 30 nm sized magnetic particles can be ca. 1 ⁇ 10 13 . This is because the smaller particles have a lower relaxivity per particle (for the same type of material), resulting in an inherent sensitivity disadvantage.
  • the magnetic particles are selected such that T 2 increases with an increase in the fraction of aggregated particles.
  • the assay of the invention can be designed to change the direction of T 2 in the presence of analyte (see FIGS. 5A-5C ).
  • the assay can be an agglomerative sandwich immunoassay in which two populations of magnetic particles bind to different epitopes of an analyte (see FIG. 5A ); a competitive assay in which analyte competes with a multivalent binding agents to inhibit the aggregation of magnetic particles (see FIG. 5B ); or a hybridization-mediated agglomeration in which two populations of magnetic particles bind to a first and second portion of an oligonucleotide (see FIG. 5C ).
  • Additional competitive format might include when two particles binding moieties bind without agglomerator (e.g. the DNA oligonucleotides are designed so that two nanoparticles have two different oligos and they can anneal together and when heated the analyte or amplicon or target DNA competes or disrupts the np annealing).
  • agglomerator e.g. the DNA oligonucleotides are designed so that two nanoparticles have two different oligos and they can anneal together and when heated the analyte or amplicon or target DNA competes or disrupts the np annealing.
  • a target sample can be incubated in the presence of a magnetic particle that has been decorated with binding moieties specific to a target analyte and a multivalent binding agent, in an inhibition assay the binding of the analyte to the magnetic particles blocks agglomeration of the magnetic particles with the multivalent binding agent;
  • a target sample can be incubated in the presence of a magnetic particle that has been decorated with binding moieties specific to a target analyte and a multivalent binding agent, in a disaggregation assay the analyte is exposed to a pre-formed aggregate of the multivalent binding agent and the magnetic particle and the analyte displaces the multivalent binding agent to reduce aggregation in the liquid sample; or
  • a target sample can be incubated in the presence of a magnetic particle that has been decorated with binding moieties specific to a target analyte and the target an
  • a multivalent binding agent e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran.
  • a carrier e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran.
  • the magnetic particles described herein include those described, e.g., in U.S. Pat. No. 7,564,245 and U.S. Patent Application Publication No. 2003-0092029, each of which is incorporated herein by reference.
  • the magnetic particles are generally in the form of conjugates, that is, a magnetic particle with one or more binding moieties (e.g., an oligonucleotide, nucleic acid, polypeptide, or polysaccharide) linked thereto.
  • the binding moiety causes a specific interaction with a target analyte.
  • the binding moiety specifically binds to a selected target analyte, for example, a nucleic acid, polypeptide, or polysaccharide.
  • binding causes aggregation of the conjugates, resulting in a change, e.g., a decrease (e.g., in the case of smaller magnetic particles) or an increase (e.g., in the case of larger magnetic particles) in the spin-spin relaxation time (T2) of adjacent water protons in an aqueous solution (or protons in a non-aqueous solvent).
  • a change e.g., a decrease (e.g., in the case of smaller magnetic particles) or an increase (e.g., in the case of larger magnetic particles) in the spin-spin relaxation time (T2) of adjacent water protons in an aqueous solution (or protons in a non-aqueous solvent).
  • the analyte binds to a preformed aggregate in a competitive disaggregation assay (e.g., an aggregate formed from a multivalent binding agent and magnetic particles), or competes with a multivalent binding agent for binding moieties on the magnetic particles in an inhibition assay (i.e., the formation of aggregates is inhibited in the presence of the analyte).
  • a competitive disaggregation assay e.g., an aggregate formed from a multivalent binding agent and magnetic particles
  • an inhibition assay i.e., the formation of aggregates is inhibited in the presence of the analyte.
  • the conjugates have high relaxivity owing to the superparamagnetism of their iron, metal oxide, or other ferro or ferrimagnetic nanomaterials.
  • Iron, cobalt, and nickel compounds and their alloys, rare earth elements such as gadolinium, and certain intermetallics such as gold and vanadium are ferromagnets can be used to produce superparamagnetic particles.
  • the magnetic particles can be monodisperse (a single crystal of a magnetic material, e.g., metal oxide, such as superparamagnetic iron oxide, per magnetic particle) or polydisperse (e.g., a plurality of crystals per magnetic particle).
  • the magnetic metal oxide can also include cobalt, magnesium, zinc, or mixtures of these metals with iron.
  • Important features and elements of magnetic particles that are useful to produce conjugates include: (i) a high relaxivity, i.e., strong effect on water (or other solvent) relaxation, (ii) a functional group to which the binding moiety can be covalently attached, (iii) a low non-specific binding of interactive moieties to the magnetic particle, and/or (iv) stability in solution, i.e., the magnetic particles remain suspended in solution, not precipitated and/or the nps retain their ability to be employed in the described method (i.e. the nps have a shelf life).
  • the magnetic particles may be linked to the binding moieties via functional groups.
  • the magnetic particles can be associated with a polymer that includes functional groups selected, in part, to enhance the magnetic particles nonspecific reversibility.
  • the polymer can be a synthetic polymer, such as, but not limited to, polyethylene glycol or silane, natural polymers, or derivatives of either synthetic or natural polymers or a combination of these.
  • the polymer may be hydrophilic.
  • the polymer “coating” is not a continuous film around the magnetic metal oxide, but is a “mesh” or “cloud” of extended polymer chains attached to and surrounding the metal oxide.
  • the polymer can include polysaccharides and derivatives, including dextran, pullanan, carboxydextran, carboxmethyl dextran, and/or reduced carboxymethyl dextran.
  • the metal oxide can be a collection of one or more crystals that contact each other, or that are individually entrapped or surrounded by the polymer.
  • the magnetic particles can be associated with non-polymeric functional group compositions.
  • Methods of synthesizing stabilized, functionalized magnetic particles without associated polymers are described, for example, in Halbreich et al., Biochimie, 80:379 (1998).
  • the magnetic particles typically include metal oxide mono and polycrystals of about 1-25 nm, e.g., about 3-10 nm, or about 5 nm in diameter per crystal.
  • the magnetic particles can also include a polymer component in the form of a core and/or coating, e.g., about 5 to 20 nm thick or more.
  • the overall size of the magnetic particles can be, e.g., from 20 to 50 nm, from 50 to 200 nm, from 100 to 300 nm, from 250 to 500 nm, from 400 to 600 nm, from 500 to 750 nm, from 700 to 1,200 nm, from 1,000 to 1,500 nm, or from 1,500 to 2,000 nm.
  • the magnetic particles may be prepared in a variety of ways. It is preferred that the magnetic particle have functional groups that link the magnetic particle to the binding moiety.
  • Carboxy functionalized magnetic particles can be made, for example, according to the method of Gorman (see PCT Publication No. WO00/61191). In this method, reduced carboxymethyl (CM) dextran is synthesized from commercial dextran. The CM-dextran and iron salts are mixed together and are then neutralized with ammonium hydroxide. The resulting carboxy functionalized magnetic particles can be used for coupling amino functionalized oligonucleotides.
  • Carboxy-functionalized magnetic particles can also be made from polysaccharide coated magnetic particles by reaction with bromo or chloroacetic acid in strong base to attach carboxyl groups.
  • carboxy-functionalized particles can be made from amino-functionalized magnetic particles by converting amino to carboxy groups by the use of reagents such as succinic anhydride or maleic anhydride.
  • Magnetic particle size can be controlled by adjusting reaction conditions, for example, by using low temperature during the neutralization of iron salts with a base as described in U.S. Pat. No. 5,262,176. Uniform particle size materials can also be made by fractionating the particles using centrifugation, ultrafiltration, or gel filtration, as described, for example in U.S. Pat. No. 5,492,814.
  • Magnetic particles can also be synthesized according to the method of Molday (Molday, R. S, and D. MacKenzie, “Immunospecific ferromagnetic iron-dextran reagents for the labeling and magnetic separation of cells,” J. Immunol. Methods, 52:353 (1982)), and treated with periodate to form aldehyde groups.
  • the aldehyde-containing magnetic particles can then be reacted with a diamine (e.g., ethylene diamine or hexanediamine), which will form a Schiff base, followed by reduction with sodium borohydride or sodium cyanoborohydride.
  • a diamine e.g., ethylene diamine or hexanediamine
  • Dextran-coated magnetic particles can be made and cross-linked with epichlorohydrin.
  • ammonia reacts with epoxy groups to generate amine groups, see Hogemann, D., et al., Improvement of MRI probes to allow efficient detection of gene expression Bioconjug. Chem., 11:941 (2000), and Josephson et al., “High-efficiency intracellular magnetic labeling with novel superparamagnetic-Tat peptide conjugates,” Bioconjug. Chem., 10:186 (1999).
  • This material is known as cross-linked iron oxide or “CLIO” and when functionalized with amine is referred to as amine-CLIO or NH 2 —CLIO.
  • Carboxy-functionalized magnetic particles can be converted to amino-functionalized magnetic particles by the use of water-soluble carbodiimides and diamines such as ethylene diamine or hexane diamine.
  • the magnetic particles can be formed from a ferrofluid (i.e., a stable colloidal suspension of magnetic particles).
  • the magnetic particle can be a composite of including multiple metal oxide crystals of the order of a few tens of nanometers in size and dispersed in a fluid containing a surfactant, which adsorbs onto the particles and stabilizes them, or by precipitation, in a basic medium, of a solution of metal ions.
  • Suitable ferrofluids are sold by the company Liquids Research Ltd.
  • WHKS1S9 (A, B or C), which is a water-based ferrofluid including magnetite (Fe 3 O 4 ), having particles 10 nm in diameter
  • WHJS1 (A, B or C)
  • BKS25 dextran which is a water-based ferrofluid stabilized with dextran, including particles of magnetite (Fe 3 O 4 ) 9 nm in diameter
  • suitable ferrofluids for use in the systems and methods of the invention are oleic acid-stabilized ferrofluids available from Ademtech, which include ca. 70% weight ⁇ -Fe 2 O 3 particles (ca. 10 nm in diameter), 15% weight octane, and 15% weight oleic acid.
  • the magnetic particles are typically a composite including multiple metal oxide crystals and an organic matrix, and having a surface decorated with functional groups (i.e., amine groups or carboxy groups) for the linking binding moieties to the surface of the magnetic particle.
  • the magnetic particles useful in the methods of the invention include those commercially available from Dynal, Seradyn, Kisker, Miltenyi Biotec, Chemicell, Anvil, Biopal, Estapor, Genovis, Thermo Fisher Scientific, JSR micro, Invitrogen, and Ademtech, as well as those described in U.S. Pat. Nos.
  • Avidin or streptavidin can be attached to magnetic particles for use with a biotinylated binding moiety, such as an oligonucleotide or polypeptide (see, e.g., Shen et al., “Magnetically labeled secretin retains receptor affinity to pancreas acinar cells,” Bioconjug. Chem., 7:311 (1996)).
  • biotin can be attached to a magnetic particle for use with an avidin-labeled binding moiety.
  • the binding moiety is covalently linked to the surface of the magnetic particle; the particles may be decorated with IgG molecules; the particles may be decorated with anti his antibodies; or the particles may be decorated with his-tagged FAbs.
  • Low molecular weight materials can be separated from the magnetic particles by ultra-filtration, dialysis, magnetic separation, or other means prior to use.
  • unreacted binding moieties and linking agents can be separated from the magnetic particle conjugates by magnetic separation or size exclusion chromatography.
  • the magnetic particles can be fractionated by size to produce mixtures of particles of a particular size range and average diameter.
  • analyte detection using T 2 relaxation assays can require selecting a proper particle to enable sufficiently sensitive analyte-induced agglomeration.
  • Higher sensitivities can be achieved using particles that contain multiple superparamagnetic iron oxide cores (5-15 nm diameter) within a single larger polymer matrix or ferrofluid assembly (100 nm-1200 nm total diameter, such as particles having an average diameter of 100 nm, 200 nm, 250 nm, 300 nm, 500 nm, 800 nm, or 1000 nm), or by using a higher magnetic moment materials or particles with higher density, and/or particles with higher iron content.
  • these types of particles provided a sensitivity gain of over 100 ⁇ due to a much higher number of iron atoms per particle, which is believed to lead to an increase in sensitivity due to the decreased number of particles present in the assay solution and possibly a higher amount of superparamagnetic iron affected by each clustering event.
  • Relaxivity per particle and particle size is one useful term for selecting an optimal particle for high sensitivity assays. Ideally, this term will be as large as possible. Relaxivity per particle is a measure of the effect of each particle on the measured T 2 value. The larger this number, the fewer the number of particles needed to elicit a given T 2 response. Furthermore, lowering the concentration of particles in the reactive solution can improve the analytical sensitivity of the assay. Relaxivity per particle can be a more useful parameter in that the iron density and relaxivity can vary from magnetic particle to magnetic particle, depending upon the components used to make the particles (see Table 1). Relaxivity per particle is proportional to the saturation magnetization of a superparamagnetic material.
  • the base particle for use in the systems and methods of the invention can be any of the commercially available particles identified in Table 2.
  • the magnetic particles for use in the systems and methods of the invention can have a hydrodynamic diameter from 10 nm to 1200 nm, and containing on average from 8 ⁇ 10 2 -1 ⁇ 10 10 metal atoms per particle, and having a relaxivity per particle of from 1 ⁇ 10 4 -1 ⁇ 10 13 mM ⁇ 1 s ⁇ 1 .
  • the magnetic particles used in the systems and methods of the invention can be any of the designs, composites, or sources described above, and can be further modified has described herein for use as a magnetic resonance switch.
  • the use of large particles may be desired to maximize iron content and the relaxivity per particle.
  • particles of this size tend to settle rapidly out of solution.
  • particle settling does not typically interfere with the assay if magnetic particle sizes are kept below 500 nm.
  • a magnetic particle size of about 100-300 nm particle is ideal for stability in terms of settling, even after functionalization (increasing the hydrodynamic diameter to 300 nm by approximately 50 nm), and to afford the high sensitivity enabled by a high relaxivity per particle.
  • Particle density certainly plays a role in buoyancy. As such, the relative density of the solution and particles plays an important role in settling of the particle. Accordingly, a possible solution to this problem is the use of buoyant magnetic particles (i.e., a hollow particle, or particle containing both a low density matrix and high density metal oxide).
  • Settling may affect the T 2 detection, thus, solution additives may be employed to change the ratio of the particle to solution density. T 2 detection can be impacted by settling if there is a significant portioning of the superparamagentic material from the measured volume of liquid. Settling can be assessed by diluting the particles to a concentration such that UV-Vis absorbance at 410 nm is between 0.6-0.8 absorbance units and then monitoring the absorbance for 90 minutes.
  • the difference between the initial and final absorbances divided by the initial absorbance will be greater than 5%. If % settling is above 5% then the particle is typically not suitable for use in assays requiring high analytical sensitivity.
  • the magnetic particles used in the assays of the invention can be, but are not limited to, nonsettling magnetic particles. High settling represents handling difficulties and may lead to reproducibility issues.
  • Nonspecific reversibility is a measure of the colloidal stability and robustness against non-specific aggregation. Nonspecific reversibility is assessed by measuring the T 2 values of a solution of particles before and after incubation in a uniform magnetic field (defined as ⁇ 5000 ppm). Starting T 2 values are typically 200 ms for a particle with an iron concentration of 0.01 mM Fe.
  • the samples are deemed reversible. Further, 10% is a threshold allowing starting T 2 measurements to reflect assay particle concentration. If the difference is greater than 10%, then the particles exhibit irreversibility in the buffer, diluents, and matrix tested.
  • the MAA reversibility of the magnetic particles can be altered as described herein. For example, colloidal stability and robustness against non-specific aggregation can be influenced by the surface characteristics of the particles, the binding moieties, the assay buffer, the matrix and the assay processing conditions. Maintenance of colloidal stability and resistance to non-specific biding can be altered by conjugation chemistry, blocking methods, buffer modifications, and/or changes in assay processing conditions.
  • the monodispersity in the size distribution of the magnetic particles used a distinction observed in polydisperse particles post-coating versus monodisperse particle pre-coating.
  • Polydisperse batches of magnetic particles can lack reproducibility and compromise sensitivity.
  • Polydisperse samples can also present problems in terms of achieving uniform coatings.
  • the magnetic particles be substantially monodisperse in size distribution (i.e., having a polydispersity index of less than about 0.8-0.9).
  • the assays of the invention can be designed to accommodate the use of polydisperse magnetic particles.
  • the assays of the invention require monitoring a shift in the clustering states of the agglomeration assays and that measuring a change in clustering likely requires a significant fraction of clustered particles (e.g., thought to be >1-10%), the total number of particles in an assay should be minimized to enable the highest sensitivity. However, sufficient number of particles must be present to allow utilization of the T 2 detection dynamic range. We have found that the highest sensitivity is observed when the number of magnetic particles (or molar equivalent) is approximately on the same order of magnitude of the number (or molar equivalent) of the analyte being detected, and the magnitude of the number (or molar equivalent) multivalent binding agents employed (i.e., in an inhibition assay).
  • the magnetic particle surface may also be required to modify the magnetic particle surface to reduce non-specific binding of background proteins to the magnetic particles.
  • Non-specific binding of background proteins to particles can induce or impede particle clustering, resulting in false signals and/or false lack of signals.
  • the surface of the magnetic particle can include blocking agents covalently linked to the surface of the magnetic particle which reduce non-specific binding of background proteins.
  • agents that one could use to achieve the desired effect, and in some cases, it is a combination of agents that is optimal (see Table 3; exemplary particles, coatings, and binding moieties).
  • NP-COOH amino Dextran Small molecule Transferrin Lysozyme BSA FSG BGG Ovalbumin amino PEG Human albumin none Antibody amino PEG BSA amino Dextran NP-amino: none Small molecule PEG NP-SA: none biotinylated Ab biotinylated amino Antibody PEG NP-SA: biotinylated amino small molecule PEG NP-anti- none Antibody species: NP-Ni: none his-tagged antibody
  • a protein block may be required to achieve assay activity and sensitivity, particularly in proteinaceous samples (e.g., plasma samples or whole blood samples), that is comparable to results in nonproteinaceous buffer samples.
  • Some commonly used protein blockers which may be used in provided preparations include, e.g., bovine serum albumin (BSA), fish skin gelatin (FSG), bovine gamma globulin (BGG), lysozyme, casein, peptidase, or non-fat dry milk.
  • BSA bovine serum albumin
  • FSG fish skin gelatin
  • BGG bovine gamma globulin
  • lysozyme casein
  • casein casein
  • peptidase or non-fat dry milk.
  • a magnetic particle coating includes BSA or FSG.
  • a combination of coatings are combinations of those exemplary coatings listed in Table 3.
  • nonspecific binding can be due to lipids or other non-proteinaceous molecules in the biological sample.
  • changes in pH and buffer ionic strength maybe selected to enhance the particle repulsive forces, but not enough to limit the results of the intended interactions.
  • the assays of the invention can include reagents for reducing the non-specific binding to the magnetic particles.
  • the assay can include one or more proteins (e.g., albumin, fish skin gelatin, lysozyme, or transferrin); low molecular weight ( ⁇ 500 Daltons) amines (e.g., amino acids, glycine, ethylamine, or mercaptoethanol amine); and/or water soluble non-ionic surface active agents (e.g., polyethyleneglycol, Tween® 20, Tween® 80, Pluronic®, or Igepal®) (see Table 4).
  • proteins e.g., albumin, fish skin gelatin, lysozyme, or transferrin
  • low molecular weight ( ⁇ 500 Daltons) amines e.g., amino acids, glycine, ethylamine, or mercaptoethanol amine
  • water soluble non-ionic surface active agents e.g., polyethylenegly
  • the surfactant may be selected from a wide variety of soluble non-ionic surface active agents including surfactants that are generally commercially available under the IGEPAL trade name from GAF Company.
  • the IGEPAL liquid non-ionic surfactants are polyethylene glycol p-isooctylphenyl ether compounds and are available in various molecular weight designations, for example, IGEPAL CA720, IGEPAL CA630, and IGEPAL CA890.
  • Other suitable non-ionic surfactants include those available under the trade name TETRONIC 909 from BASF Wyandotte Corporation. This material is a tetra-functional block copolymer surfactant terminating in primary hydroxyl groups.
  • Suitable non-ionic surfactants are also available under the VISTA ALPHONIC trade name from Vista Chemical Company and such materials are ethoxylates that are non-ionic biodegradables derived from linear primary alcohol blends of various molecular weights.
  • the surfactant may also be selected from poloxamers, such as polyoxyethylene-polyoxypropylene block copolymers, such as those available under the trade names Synperonic PE series (ICI), Pluronic® series (BASF), Supronic, Monolan, Pluracare, and Plurodac, polysorbate surfactants, such as Tween® 20 (PEG-20 sorbitan monolaurate), and glycols such as ethylene glycol and propylene glycol.
  • poloxamers such as polyoxyethylene-polyoxypropylene block copolymers, such as those available under the trade names Synperonic PE series (ICI), Pluronic® series (BASF), Supronic, Monolan, Pluracare, and Plurodac
  • non-ionic surfactants may be selected to provide an appropriate amount of detergency for an assay without having a deleterious effect on assay reactions.
  • surfactants may be included in a reaction mixture for the purpose of suppressing non-specific interactions among various ingredients of the aggregation assays of the invention.
  • the non-ionic surfactants are typically added to the liquid sample prior in an amount from 0.01% (w/w) to 5% (w/w).
  • the non-ionic surfactants may be used in combination with one or more proteins (e.g., albumin, fish skin gelatin, lysozyme, or transferrin) also added to the liquid sample prior in an amount from 0.01% (w/w) to 5% (w/w).
  • proteins e.g., albumin, fish skin gelatin, lysozyme, or transferrin
  • the assays, methods, and cartridge units of the invention can include additional suitable buffer components (e.g., Tris base, selected to provide a pH of about 7.8 to 8.2 in the reaction milieu); and chelating agents to scavenge cations (e.g., EDTA disodium, ethylene diamine tetraacetic acid (EDTA), citric acid, tartaric acid, glucuronic acid, saccharic acid or suitable salts thereof).
  • Tris base selected to provide a pH of about 7.8 to 8.2 in the reaction milieu
  • chelating agents to scavenge cations e.g., EDTA disodium, ethylene diamine tetraacetic acid (EDTA), citric acid, tartaric acid, glucuronic acid, saccharic acid or suitable salts thereof.
  • a binding moiety is a molecule, synthetic or natural, that specifically binds or otherwise links to, e.g., covalently or non-covalently binds to or hybridizes with, a target molecule, or with another binding moiety (or, in certain embodiments, with an aggregation inducing molecule).
  • the binding moiety can be an antibody directed toward an antigen or any protein-protein interaction.
  • the binding moiety can be a polysaccharide that binds to a corresponding target or a synthetic oligonucleotide that hybridizes to a specific complementary nucleic acid target.
  • the binding moieties can be designed or selected to serve, when bound to another binding moiety, as substrates for a target molecule such as enzyme in solution.
  • Binding moieties include, for example, oligonucleotide binding moieties (DNA, RNA, or substituted or derivatized nucleotide substitutes), polypeptide binding moieties, antibody binding moieties, aptamers, and polysaccharide binding moieties.
  • the binding moieties are oligonucleotides, attached/linked to the magnetic particles using any of a variety of chemistries, by a single, e.g., covalent, bond, e.g., at the 3′ or 5′ end to a functional group on the magnetic particle.
  • binding moieties can be used in the systems, devices, and methods of the invention to detect mutations (e.g., SNPs, translocations, large deletions, small deletions, insertions, substitutions) or to monitor gene expression (e.g., the presence of expression, or changes in the level of gene expression, monitoring RNA transcription), or CHP analysis characteristic of the presence of a pathogen, disease state, or the progression of disease.
  • An oligonucleotide binding moiety can be constructed using chemical synthesis.
  • a double-stranded DNA binding moiety can be constructed by enzymatic ligation reactions using procedures known in the art.
  • a nucleic acid e.g., an oligonucleotide
  • the nucleic acid also can be produced biologically using an expression vector into which a nucleic acid has been subcloned.
  • One method uses at least two populations of oligonucleotide magnetic particles, each with strong effects on water (or other solvent) relaxation.
  • the oligonucleotide-magnetic particle conjugates react with a target oligonucleotide, they form aggregates (e.g., clusters of magnetic particles).
  • the aggregates Upon prolonged standing, e.g., overnight at room temperature, the aggregates form large clusters (micron-sized clusters).
  • the formation of large clusters can be accomplished more quickly by employing multiple cycles of magnetic assisted agglomeration.
  • Magnetic resonance is used to determine the relaxation properties of the solvent, which are altered when the mixture of magnetic oligonucleotide magnetic particles reacts with a target nucleic acid to form aggregates.
  • Certain embodiments employ a mixture of at least two types of magnetic metal oxide magnetic particles, each with a specific sequence of oligonucleotide, and each with more than one copy of the oligonucleotide attached, e.g., covalently, per magnetic particle.
  • the assay protocol may involve preparing a mixture of populations of oligonucleotide-magnetic particle conjugates and reacting the mixture with a target nucleic acid.
  • oligonucleotide-magnetic particle conjugates can be reacted with the target in a sequential fashion.
  • Certain embodiments feature the use of magnetic resonance to detect the reaction of the oligonucleotide-magnetic particle conjugates with the target nucleic acid. When a target is present, the dispersed conjugates self-assemble to form small aggregates.
  • oligonucleotide binding moieties can be linked to the metal oxide through covalent attachment to a functionalized polymer or to non-polymeric surface-functionalized metal oxides.
  • the magnetic particles can be synthesized according to the method of Albrecht et al., Biochimie, 80:379 (1998). Dimercapto-succinic acid is coupled to the iron oxide and provides a carboxyl functional group.
  • oligonucleotides are attached to magnetic particles via a functionalized polymer associated with the metal oxide.
  • the polymer is hydrophilic.
  • the conjugates are made using oligonucleotides that have terminal amino, sulfhydryl, or phosphate groups, and superparamagnetic iron oxide magnetic particles bearing amino or carboxy groups on a hydrophilic polymer. There are several methods for synthesizing carboxy and amino derivatized-magnetic particles.
  • oligonucleotides are attached to a particle via ligand-protein binding interaction, such as biotin-streptavidin, where the ligand is covalently attached to the oligonucleotide and the protein to the particle, or vice versa.
  • ligand-protein binding interaction such as biotin-streptavidin
  • oligonucleotides are single-stranded RNA or DNA oligonucleotides 15 to 60 base in length that in solution form intramolecular interactions that fold the linear nucleic acid molecule into a three dimensional complex that then can bind with high affinity to specific molecular targets; often with equilibrium constants in the range of 1 pM to 1 nM which is similar to some monoclonal antibodies-antigen interactions.
  • Aptamers can specifically bind to other nucleic acid molecules, proteins, small organic compounds, small molecules, and cells (organisms or pathogens).
  • the binding moiety is a polypeptide (i.e., a protein, polypeptide, or peptide), attached, using any of a variety of chemistries, by a single covalent bond in such a manner so as to not affect the biological activity of the polypeptide.
  • attachment is done through the thiol group of single reactive cysteine residue so placed that its modification does not affect the biological activity of the polypeptide.
  • linear polypeptides with cysteine at the C-terminal or N-terminal end, provides a single thiol in a manner similar to which alkanethiol supplies a thiol group at the 3′ or 5′ end of an oligonucleotide.
  • Similar bifunctional conjugation reagents such as SPDP and reacting with the amino group of the magnetic particle and thiol group of the polypeptide, can be used with any thiol bearing binding moiety.
  • the types of polypeptides used as binding moieties can be antibodies, antibody fragments, and natural and synthetic polypeptide sequences.
  • the peptide binding moieties have a binding partner, that is, a molecule to which they selectively bind.
  • polypeptides can be engineered to have uniquely reactive residues, distal from the residues required for biological activity, for attachment to the magnetic particle.
  • the reactive residue can be a cysteine thiol, an N-terminal amino group, a C-terminal carboxyl group or a carboxyl group of aspartate or glutamate, etc.
  • a single reactive residue on the peptide is used to insure a unique site of attachment.
  • the binding moieties can also contain amino acid sequences from naturally occurring (wild-type) polypeptides or proteins.
  • the natural polypeptide may be a hormone, (e.g., a cytokine, a growth factor), a serum protein, a viral protein (e.g., hemagglutinin), an extracellular matrix protein, a lectin, or an ectodomain of a cell surface protein.
  • a ligand binding protein such as streptavidin or avidin that bind biotin.
  • the resulting binding moiety-magnetic particle is used to measure the presence of analytes in a test media reacting with the binding moiety.
  • a polypeptide binding moiety can be used in a universal reagent configuration, where the target of the binding moiety (e.g., small molecule, ligand, or binding partner) is pre-attached to the target analyte to create a labeled analyte that, in the presence of the polypeptide decorated particles, induces clustering.
  • target of the binding moiety e.g., small molecule, ligand, or binding partner
  • protein hormones which can be utilized as binding moieties include, without limitation, platelet-derived growth factor (PDGF), which binds the PDGF receptor; insulin-like growth factor-I and -II (Igf), which binds the lgf receptor; nerve growth factor (NGF), which binds the NGF receptor; fibroblast growth factor (FGF), which binds the FGF receptor (e.g., aFGF and bFGF); epidermal growth factor (EGF), which binds the EGF receptor; transforming growth factor (TGF, e.g., TGF ⁇ and TGF- ⁇ ), which bind the TGF receptor; erythropoietin, which binds the erythropoitin receptor; growth hormone (e.g., human growth hormone), which binds the growth hormone receptor; and proinsulin, insulin, A-chain insulin, and B-chain insulin, which all bind to the insulin receptor.
  • PDGF platelet-derived growth factor
  • Igf insulin-like
  • Receptor binding moieties are useful for detecting and imaging receptor clustering on the surface of a cell.
  • Useful ectodomains include those of the Notch protein, Delta protein, integrins, cadherins, and other cell adhesion molecules.
  • polypeptide binding moieties include immunoglobulin binding moieties that include at least one immunoglobulin domain, and typically at least two such domains.
  • An “immunoglobulin domain” refers to a domain of an antibody molecule, e.g., a variable or constant domain.
  • An “immunoglobulin superfamily domain” refers to a domain that has a three-dimensional structure related to an immunoglobulin domain, but is from a non-immunoglobulin molecule. Immunoglobulin domains and immunoglobulin superfamily domains typically include two ⁇ -sheets formed of about seven ⁇ -strands, and a conserved disulfide bond (see, e.g., Williams and Barclay Ann. Rev Immunol., 6:381 (1988)). Proteins that include domains of the Ig superfamily domains include T cell receptors, CD4, platelet derived growth factor receptor (PDGFR), and intercellular adhesion molecule (ICAM).
  • antibody refers to a full-length, two-chain immunoglobulin molecule and an antigen-binding portion and fragments thereof, including synthetic variants.
  • a typical antibody includes two heavy (H) chain variable regions (abbreviated herein as VH), and two light (L) chain variable regions (abbreviated herein as VL).
  • VH heavy chain variable regions
  • VL light chain variable regions
  • the VH and VL regions can be further subdivided into regions of hypervariability, termed “complementarity determining regions” (CDR), interspersed with regions that are more conserved, termed “framework regions” (FR).
  • CDR complementarity determining regions
  • FR framework regions
  • Each VH and VL is composed of three CDR's and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
  • An antibody can also include a constant region as part of a light or heavy chain.
  • Light chains can include a kappa or lambda constant region gene at the COOH-terminus (termed CL).
  • Heavy chains can include, for example, a gamma constant region (IgG1, IgG2, IgG3, IgG4; encoding about 330 amino acids).
  • a gamma constant region can include, e.g., CH1, CH2, and CH3.
  • full-length antibody refers to a protein that includes one polypeptide that includes VL and CL, and a second polypeptide that includes VH, CH1, CH2, and CH3.
  • antigen-binding fragment of an antibody, as used herein, refers to one or more fragments of a full-length antibody that retain the ability to specifically bind to a target.
  • antigen-binding fragments include, but are not limited to: (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) an F(ab′) 2 fragment, a bivalent fragment including two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CH1 domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., Nature 341:544 (1989)), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR).
  • CDR complementarity determining region
  • the two domains of the Fv fragment, VL and VH are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al., Science 242:423 (1988); and Huston et al., Proc. Natl. Acad. Sci. USA, 85:5879 (1988)).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also encompassed within the term “antigen-binding fragment.”
  • a single domain antibody is an antibody fragment consisting of a single monomeric variable antibody domain, and may also be used in the systems and methods of the invention. Like a whole antibody, sdAbs are able to bind selectively to a specific antigen. With a molecular weight of only 12-15 kDa, single domain antibodies are much smaller than common antibodies (150-160 kDa) which are composed of two heavy protein chains and two light chains, and even smaller than Fab fragments ( ⁇ 50 kDa, one light chain and half a heavy chain) and single-chain variable fragments ( ⁇ 25 kDa, two variable domains, one from a light and one from a heavy chain).
  • the binding moiety is a polysaccharide, linked, for example, using any of a variety of chemistries, by a single bond, e.g., a covalent bond, at one of the two ends, to a functional group on the magnetic particle.
  • the polysaccharides can be synthetic or natural.
  • Mono-, di-, tri- and polysaccharides can be used as the binding moiety. These include, e.g., glycosides, N-glycosylamines, O-acyl derivatives, O-methyl derivatives, osazones, sugar alcohols, sugar acids, sugar phosphates when used with appropriate attachment chemistry to the magnetic particle.
  • a method of accomplishing linking is to couple avidin to a magnetic particle and react the avidin-magnetic particle with commercially available biotinylated polysaccharides, to yield polysaccharide-magnetic particle conjugates.
  • biotinylated polysaccharides are commercially available as biotinylated reagents and will react with avidin-CLIO (see Syntesome, Deutschen furella Biochemie mbH.).
  • the sialyl Lewis ⁇ tetrasaccharide (Sle x ) is recognized by proteins known as Selectins, which are present on the surfaces of leukocytes and function as part of the inflammatory cascade for the recruitment of leukocytes.
  • targeting moieties include a non-proteinaceous element, e.g., a glycosyl modification (such as a Lewis antigen) or another non-proteinaceous organic molecule. Another method is covalent coupling of the protein to the magnetic particle.
  • Another feature of the methods includes identification of specific cell types, for hematological or histopatholgical investigations for example CD4/CD3 cell counts and circulating tumor cells using any of the binding moieties described above.
  • the assays of the invention can include a multivalent binding agent (i) bearing multiple analytes are linked to a carrier (e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran), or bearing multiple epitopes for binding to, for example, two or more populations of magnetic particles to form an aggregate.
  • a carrier e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran
  • multivalent binding agent multiple analytes can be linked to a carrier (e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran).
  • a carrier e.g., a simple synthetic scaffold, or a larger carrier protein or polysaccharide, such as BSA, transferrin, or dextran.
  • the multivalent binding agent can be a nucleic acid designed to bind to two or more populations of magnetic particles.
  • Such multivalent binding agents act as agglomerants and the assay architecture is characterized by a competition between the analyte being detected and the multivalent binding agent (e.g., in an inhibition assay, competition assay, or disaggregation assay).
  • the functional group, present in the analyte can be used to form a covalent bond with the carrier.
  • the analyte can be derivatized to provide a linker (i.e., a spacer separating the analyte from the carrier in the conjugate) terminating in a functional group (i.e., an alcohol, an amine, a carboxyl group, a sulfhydryl group, or a phosphate group), which is used to form the covalent linkage with the carrier.
  • a linker i.e., a spacer separating the analyte from the carrier in the conjugate
  • a functional group i.e., an alcohol, an amine, a carboxyl group, a sulfhydryl group, or a phosphate group
  • the covalent linking of an analyte and a carrier may be effected using a linker which contains reactive moieties capable of reaction with such functional groups present in the analyte and the carrier.
  • a hydroxyl group of the analyte may react with a carboxyl group of the linker, or an activated derivative thereof, resulting in the formation of an ester linking the two.
  • N-Maleimide derivatives are also considered selective towards sulfhydryl groups, but may additionally be useful in coupling to amino groups under certain conditions.
  • Reagents such as 2-iminothiolane (Traut et al., Biochemistry 12:3266 (1973)), which introduce a thiol group through conversion of an amino group, may be considered as sulfhydryl reagents if linking occurs through the formation of disulphide bridges.
  • reactive moieties capable of reaction with amino groups include, for example, alkylating and acylating agents.
  • Representative alkylating agents include:
  • ⁇ -haloacetyl compounds which show specificity towards amino groups in the absence of reactive thiol groups and are of the type XCH 2 CO— (where X ⁇ Cl, Br or I), for example, as described by Wong, Biochemistry 24:5337 (1979);
  • N-maleimide derivatives which may react with amino groups either through a Michael type reaction or through acylation by addition to the ring carbonyl group, for example, as described by Smyth et al., J. Am. Chem. Soc. 82:4600 (1960) and Biochem. J.
  • Representative amino-reactive acylating agents include: (i) isocyanates and isothiocyanates, particularly aromatic derivatives, which form stable urea and thiourea derivatives respectively; (ii) sulfonyl chlorides, which have been described by Herzig et al., Biopolymers 2:349 (1964); (iii) acid halides; (iv) active esters such as nitrophenylesters or N-hydroxysuccinimidyl esters; (v) acid anhydrides such as mixed, symmetrical, or N-carboxyanhydrides; (vi) other useful reagents for amide bond formation, for example, as described by M.
  • acylazides e.g. wherein the azide group is generated from a preformed hydrazide derivative using sodium nitrite, as described by Wetz et al., Anal. Biochem. 58:347 (1974); and (viii) imidoesters, which form stable amidines on reaction with amino groups, for example, as described by Hunter and Ludwig, J. Am. Chem. Soc. 84:3491 (1962).
  • Aldehydes and ketones may be reacted with amines to form Schiff's bases, which may advantageously be stabilized through reductive amination.
  • Alkoxylamino moieties readily react with ketones and aldehydes to produce stable alkoxamines, for example, as described by Webb et al., Bioconjugate Chem. 1:96 (1990).
  • reactive moieties capable of reaction with carboxyl groups include diazo compounds such as diazoacetate esters and diazoacetamides, which react with high specificity to generate ester groups, for example, as described by Herriot, Adv. Protein Chem. 3:169 (1947).
  • Carboxyl modifying reagents such as carbodiimides, which react through O-acylurea formation followed by amide bond formation, may also be employed.
  • functional groups in the analyte and/or the carrier may, if desired, be converted to other functional groups prior to reaction, for example, to confer additional reactivity or selectivity.
  • methods useful for this purpose include conversion of amines to carboxyls using reagents such as dicarboxylic anhydrides; conversion of amines to thiols using reagents such as N-acetylhomocysteine thiolactone, S-acetylmercaptosuccinic anhydride, 2-iminothiolane, or thiol-containing succinimidyl derivatives; conversion of thiols to carboxyls using reagents such as ⁇ -haloacetates; conversion of thiols to amines using reagents such as ethylenimine or 2-bromoethylamine; conversion of carboxyls to amines using reagents such as carbodiimides followed by diamines; and conversion of alcohols to
  • linker will include two or more reactive moieties, as described above, connected by a spacer element. The presence of such a spacer permits bifunctional linkers to react with specific functional groups within the analyte and the carrier, resulting in a covalent linkage between the two.
  • the reactive moieties in a linker may be the same (homobifunctional linker) or different (heterobifunctional linker, or, where several dissimilar reactive moieties are present, heteromultifunctional linker), providing a diversity of potential reagents that may bring about covalent attachment between the analyte and the carrier.
  • Spacer elements in the linker typically consist of linear or branched chains and may include a C 1-10 alkyl, a heteroalkyl of 1 to 10 atoms, a C 2-10 alkene, a C 2-10 alkyne, C 5-10 aryl, a cyclic system of 3 to 10 atoms, or —(CH 2 CH 2 O) n CH 2 CH 2 —, in which n is 1 to 4.
  • a multivalent binding agent will include 2, 3, 4, 5, 6, 7, 8, 15, 50, or 100 (e.g., from 3 to 100, from 3 to 30, from 4 to 25, or from 6 to 20) conjugated analytes.
  • the multivalent binding agents are typically from 10 kDa to 200 kDa in size and can be prepared as described in the Examples.
  • Embodiments of the invention include devices, systems, and/or methods for detecting and/or measuring the concentration of one or more analytes in a sample (e.g., a protein, a peptide, an enzyme, a polypeptide, an amino acid, a nucleic acid, an oligonucleotide, a therapeutic agent, a metabolite of a therapeutic agent, RNA, DNA, circulating DNA (e.g., from a cell, tumor, pathogen, or fetus), an antibody, an organism, a virus, bacteria, a carbohydrate, a polysaccharide, glucose, a lipid, a gas (e.g., oxygen and/or carbon dioxide), an electrolyte (e.g., sodium, potassium, chloride, bicarbonate, BUN, magnesium, phosphate, calcium, ammonia, and/or lactate), general chemistry molecules (creatinine, glucose), a lipoprotein, cholesterol, a fatty acid, a glycoprotein,
  • the analytes may include identification of cells or specific cell types.
  • the analyte(s) may include one or more biologically active substances and/or metabolite(s), marker(s), and/or other indicator(s) of biologically active substances.
  • a biologically active substance may be described as a single entity or a combination of entities.
  • biologically active substance includes without limitation, medications; vitamins; mineral supplements; substances used for the treatment, prevention, diagnosis, cure or mitigation of disease or illness; or substances which affect the structure or function of the body; or pro-drugs, which become biologically active or more active after they have been placed in a predetermined physiological environment; or biologically toxic agents such as those used in biowarfare including organisms such as anthrax, ebola, Salmonella typhimurium, Marburg virus, plague, cholera, Francisella tulariesis (tularemia), brucellosis, Q fever, Venezuelan hemorrhagic fever, Coccidioides mycosis, glanders, Melioidosis, Shigella , Rocky Mountain spotted fever, typhus, Psittacosis, yellow fever, Japanese B encephalitis, Rift Valley fever, and smallpox; naturally-occurring toxins that can be used as weapons include ricin, aflatoxin, SEB, botulinum toxin, saxit
  • Analytes may also include organisms such as Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis , Coagulase negative Staphalococcus, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, Aspergillus fumigates, Bacteroides fragilis, Bacteroides fragilis , blaSHV, Burkholderia cepacia, Campylobacter jejuni/coli, Candida guilliermondii, Candida lusitaniae, Clostridium pefringens, Enterobacter aeraogenesl, Enterobacter cloacae , Enterobacteriaceae spp., Haemophilus influenza, Kingella kingae, Klebs
  • Analytes may also include viral organisms such as dsDNA viruses (e.g., adenoviruses, herpes viruses, poxviruses); ssDNA viruses (+)sense DNA (e.g., parvoviruses); dsRNA viruses (e.g., reoviruses); (+)ssRNA viruses (+)sense RNA (e.g., picornaviruses, togaviruses); ( ⁇ )ssRNA viruses ( ⁇ )sense RNA (e.g., orthomyxoviruses, rhabdoviruses); ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g., retroviruses); and dsDNA-RT viruses (e.g., hepadnaviruses).
  • dsDNA viruses e.g., adenoviruses, herpes viruses, poxviruses
  • ssDNA viruses (+)sense DNA e.g., par
  • Opportunistic infections which can be detected using the systems and methods of the invention include, without limitation, fungal, viral, bacterial, protozoan infections, such as: 1) fungal infections, such as those by Candida spp. (drug resistant and non-resistant strains), C. albicans, C. krusei, C. glabrata , and Aspergillus fumigates; 2) gram negative infections, such as those by E. coli, Stenotrophomonas maltophilia, Klebsiella pneumonia/oxytoca , and Pseudomonas aeruginosa ; and 3) gram positive infections, such as those by Staphylococcus spp., S. aureus, S.
  • the infection can be by coagulase negative staphylococcus, Corynebacterium spp., Fusobacterium spp., Morganella morganii, Pneumocystis jirovecii (previously known as Pneumocystis carinii ), F. hominis, S.
  • polyomavirus JC polyomavirus the virus that causes progressive multifocal leukoencephalopathy
  • Acinetobacter baumanni the virus that causes progressive multifocal leukoencephalopathy
  • Toxoplasma gondii the virus that causes progressive multifocal leukoencephalopathy
  • cytomegalovirus the virus that causes progressive multifocal leukoencephalopathy
  • Aspergillus spp. Kaposi's Sarcoma
  • Cryptosporidium spp. Cryptococcus neoformans
  • Histoplasma capsulatum the virus that causes progressive multifocal leukoencephalopathy
  • Non-limiting examples of broad categories of analytes which can be detected using the devices, systems, and methods of the invention include, without limitation, the following therapeutic categories: anabolic agents, antacids, anti-asthmatic agents, anti-cholesterolemic and anti-lipid agents, anti-coagulants, anti-convulsants, anti-diarrheals, anti-emetics, anti-infective agents, anti-inflammatory agents, anti-manic agents, anti-nauseants, anti-neoplastic agents, anti-obesity agents, anti-pyretic and analgesic agents, anti-spasmodic agents, anti-thrombotic agents, anti-uricemic agents, anti-anginal agents, antihistamines, anti-tussives, appetite suppressants, biologicals, cerebral dilators, coronary dilators, decongestants, diuretics, diagnostic agents, erythropoietic agents, expectorants, gastrointestinal sedatives, hyperglycemic agents, hypnotics
  • analytes which can be detected using the devices, systems, and methods of the invention include, without limitation, the following therapeutic categories: analgesics, such as nonsteroidal anti-inflammatory drugs, opiate agonists and salicylates; antihistamines, such as H 1 -blockers and H 2 -blockers; anti-infective agents, such as anthelmintics, antianaerobics, antibiotics, aminoglycoside antibiotics, antifungal antibiotics, cephalosporin antibiotics, macrolide antibiotics, miscellaneous ⁇ -lactam antibiotics, penicillin antibiotics, quinolone antibiotics, sulfonamide antibiotics, tetracycline antibiotics, antimycobacterials, antituberculosis antimycobacterials, antiprotozoals, antimalarial antiprotozoals, antiviral agents, antiretroviral agents, scabicides, and urinary anti-infectives; antineoplastic agents, such as al
  • NSAIDs nonsteroidal anti-inflammatory drugs
  • analgesics such as diclofenac, ibuprofen, ketoprofen, and naproxen
  • opiate agonist analgesics such as codeine, fentanyl, hydromorphone, and morphine
  • salicylate analgesics such as aspirin (ASA) (enteric coated ASA)
  • H 1 -blocker antihistamines such as clemastine and terfenadine
  • H 2 -blocker antihistamines such as cimetidine, famotidine, nizadine, and ranitidine
  • anti-infective agents such as mupirocin
  • antianaerobic anti-infectives such as chloramphenicol and clindamycin
  • antifungal antibiotic anti-infectives such as amphotericin b
  • biologically active substances from the above categories include, without limitation, antineoplastics such as androgen inhibitors, antimetabolites, cytotoxic agents, and immunomodulators; anti-tussives such as dextromethorphan, dextromethorphan hydrobromide, noscapine, carbetapentane citrate, and chlorphedianol hydrochloride; antihistamines such as chlorpheniramine maleate, phenindamine tartrate, pyrilamine maleate, doxylamine succinate, and phenyltoloxamine citrate; decongestants such as phenylephrine hydrochloride, phenylpropanolamine hydrochloride, pseudoephedrine hydrochloride, and ephedrine; various alkaloids such as codeine phosphate, codeine sulfate and morphine; mineral supplements such as potassium chloride, zinc chloride, calcium carbonates, magnesium oxide
  • Radiosensitizers such as metoclopramide, sensamide or neusensamide (manufactured by Oxigene); profiromycin (made by Vion); RSR13 (made by Allos); Thymitaq (made by Agouron), etanidazole or lobenguane (manufactured by Nycomed); gadolinium texaphrin (made by Pharmacyclics); BuDR/Broxine (made by NeoPharm); IPdR (made by Sparta); CR2412 (made by Cell Therapeutic); L1X (made by Terrapin); or the like.
  • radiosensitizers such as metoclopramide, sensamide or neusensamide (manufactured by Oxigene); profiromycin (made by Vion); RSR13 (made by Allos); Thymitaq (made by Agouron), etanidazole or lobenguane (manufactured by Nycomed); ga
  • Biologically active substances which can be detected using the devices, systems, and methods of the invention include, without limitation, medications for the gastrointestinal tract or digestive system, for example, antacids, reflux suppressants, antiflatulents, antidoopaminergics, proton pump inhibitors, H 2 -receptor antagonists, cytoprotectants, prostaglandin analogues, laxatives, antispasmodics, antidiarrheals, bile acid sequestrants, and opioids; medications for the cardiovascular system, for example, beta-receptor blockers, calcium channel blockers, diuretics, cardiac glycosides, antiarrhythmics, nitrate, antianginals, vascoconstrictors, vasodilators, peripheral activators, ACE inhibitors, angiotensin receptor blockers, alpha blockers, anticoagulants, heparin, HSGAGs, antiplatelet drugs, fibrinolytics, anti-hemophilic factors, haemostatic drugs, hypolipaemic agents, and statin
  • pain medications e.g., analgesics
  • opioids such as buprenorphine, butorphanol, dextropropoxyphene, dihydrocodeine, fentanyl, diamorphine (heroin), hydromorphone, morphine, nalbuphine, oxycodone, oxymorphone, pentazocine, pethidine (meperidine), and tramadol
  • salicylic acid and derivatives such as acetylsalicylic acid (aspirin), diflunisal, and ethenzamide
  • pyrazolones such as aminophenazone, metamizole, and phenazone
  • anilides such as paracetamol (acetaminophen), phenacetin; and others such as ziconotide and tetradyrocannabinol.
  • blood pressure medications e.g., antihypertensives and diuretics
  • antiadrenergic agents such as clonidine, doxazosin, guanethidine, guanfacine, mecamylamine, methyldopa, moxonidinie, prazosin, rescinnamine, and reserpine
  • vasodilators such as diazoxide, hydralazine, minoxidil, and nitroprusside
  • low ceiling diuretics such as bendroflumethiazide, chlorothiazide, chlortalidone, hydrochlorothiazide, indapamide, quinethazone, mersalyl, metolazone, and theobromine
  • high ceiling diuretics such as bumetanide, furosemide, and torasemide
  • potassium-sparing diuretics such as amiloride, eplerenone,
  • anti-thrombotics e.g., thrombolytics, anticoagulants, and antiplatelet drugs
  • vitamin K antagonists such as acenocoumarol, clorindione, dicumarol, diphenadione, ethyl biscoumacetate, phenprocoumon, phenindione, tioclomarol, and warfarin
  • heparin group platelet aggregation inhibitors
  • platelet aggregation inhibitors such as antithrombin III, bemiparin, dalteparin, danaparoid, enoxaparin, heparin, nadroparin, parnaparin, reviparin, sulodexide, and tinzaparin
  • other platelet aggregation inhibitors such as abciximab, acetylsalicylic acid (aspirin), aloxiprin, beraprost, ditazole, carbasalate calcium,
  • anticonvulsants which can be detected using the devices, systems, and methods of the invention include barbiturates such as barbexaclone, metharbital, methylphenobarbital, phenobarbital, and primidone; hydantoins such as ethotoin, fosphenyloin, mephenyloin, and phenyloin; oxazolidinediones such as ethadione, paramethadione, and trimethadione; succinimides such as ethosuximide, mesuximide, and phensuximide; benzodiazepines such as clobazam, clonazepam, clorazepate, diazepam, lorazepam, midazolam, and nitrazepam; carboxamides such as carbamazepine, oxcarbazepine, rufinamide; fatty acid derivatives such as valpromide and
  • anti-cancer agents which can be detected using the devices, systems, and methods of the invention include acivicin; aclarubicin; acodazole hydrochloride; acronine; adriamycin; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; car
  • Embodiments of the invention may be used in the monitoring of one or more analytes in the diagnosis, management, and/or treatment of any of a wide range of medical conditions.
  • Various categories of medical conditions include, for example, disorders of pain; of alterations in body temperature (e.g., fever); of nervous system dysfunction (e.g., syncope, myalgias, movement disorders, numbness, sensory loss, delirium, dementia, memory loss, or sleep disorders); of the eyes, ears, nose, and throat; of circulatory and/or respiratory functions (e.g., dyspinea, pulmonary edema, cough, hemoptysis, hypertension, myocardial infarctions, hypoxia, cyanosis, cardiovascular collapse, congestive heart failure, edema, or shock); of gastrointestinal function (e.g., dysphagia, diarrhea, constipation, GI bleeding, jaundice, ascites, indigestion, nasusea, vomiting); of renal and urinary tract
  • oncology e.g., neoplasms, malignancies, angiogenesis, paraneoplasic syndromes, or oncologic emergencies
  • hematology e.g., anemia, hemoglobinopathies, megalooblastic anemias, hemolytic anemias, aplastic anemia, myelodysplasia, bone marrow failure, polycythemia vera, myloproliferative diseases, acute myeloid leukemia, chronic myeloid leukemia, lymphoid malignancies, plasma cell disorders, transfusion biology, or transplants
  • hemostasis e.g., disorders of coagulation and thrombosis, or disorders of the platelet and vessel wall
  • infectious diseases e.g., sepsis, septic shock, fever of unknown origin, endocardidtis, bites, burns, osteomyelitis, abscesses, food poisoning, pelvic inflammatory disease, bacterial (e.g., bacterial), bacterial (e.
  • Medical tests e.g., blood tests, urine tests, and/or other human or animal tissue tests
  • medical tests include, for example, general chemistry tests (e.g., analytes include albumin, blood urea nitrogen, calcium, creatinine, magnesium, phosphorus, total protein, and/or uric acid); electrolyte tests (e.g., analytes include sodium, potassium, chloride, and/or carbon dioxide); diabetes tests (e.g., analytes include glucose, hemoglobin A 1C, and/or microalbumin); lipids tests (e.g., analytes include apolipoprotein A1, apolipoprotein B, cholesterol, triglyceride, low density lipoprotein cholesteral, and/or high density lipoprotein cholesterol); nutritional assessment (e.g., analytes include albumin, prealbumin, transferrin, retinol binding protein, alpha1-acid glycoprotein, and/or ferritin
  • Specific cancer markers that can be detected using the methods, devices, cartridges, and kits of the invention include, without limitation, 17-beta-hydroxysteroid dehydrogenase type 1, Abl interactor 2, Actin-related protein 2 ⁇ 3 complex subunit 1A, Albumin, Aldolase A, Alkaline phosphatase, placental type, Alpha 1 antitrypsin, Alpha-1-acid glycoprotein 1, Alpha-2-HS-glycoprotein, Alpha lactalbumin, Alpha-2-macroglobulin, Alpha-fetoprotein (AFP), Angiogenin ribonuclease RNase A family 5, Angiopoietin 1, Angiopoietin 2, Antigen identified by monoclonal antibody Ki-67, Antileukoproteinase 1(SLPI), Apolipoprotein A1, ATP7B, ⁇ 2-microglobulin, B-cell CLL/lymphoma 2, BCL2-associated X protein, BRCA1, BRCA2, BrMS1, Butyrate-induced transcript 1, CA15
  • kits, cartridges, and systems of the invention can be configured to detect a predetermined combination panel of analytes that may be used to understand the medical condition of the subject.
  • a combination panel may include detection of pathogens, therapeutic agents used to treat the suspected pathogen/s, and a potential biomarker to monitor the therapeutic pharmacologic progress (efficacy or pharmacokinetic), or monitoring the presence of the pathogen or pathogen by-products.
  • a disease treatment panel configured for use to detect a disease or a disease biomarker, the level or concentration of a therapeutic drug for use in treating the suspected disease, a potential biomarker to monitor the therapeutic pharmacologic progress (efficacy or pharmacokinetic), and general chemistry biomarker or other physiological marker of the disease or effect of treatment.
  • a disease treatment panel configured for use to detect a disease or a disease biomarker, the level or concentration of a therapeutic drug for use in treating the suspected disease, a potential biomarker to monitor the therapeutic pharmacologic progress (efficacy or pharmacokinetic), and general chemistry biomarker or other physiological marker of the disease or effect of treatment.
  • the systems and methods of the invention can be used to monitor immuno-compromised subjects following allogenic transplantation.
  • transplant subjects that receive solid organ, bone marrow, hematopoietic stem cell, or other allogeneic donations, there is a need to monitor the immune status, organ function, and if necessary, rapidly and accurately identify opportunistic infections.
  • Tacrolimus also FK-506, Prograf, or Fujimycin
  • IL-2 interleukin-2
  • Tacrolimus is normally prescribed as part of a post-transplant cocktail including steroids, mycophenolate and IL-2 receptor inhibitors. Dosages are titrated to target blood levels. Side effects can be severe and include infection, cardiac damage, hypertension, blurred vision, liver and kidney problems, seizures, tremors, hyperkalemia, hypomagnesaemia, hyperglycemia, diabetes mellitus, itching, insomnia, and neurological problems such as confusion, loss of appetite, weakness, depression, cramps, and neuropathy. In addition tacrolimus may potentially increase the severity of existing fungal or infectious conditions such as herpes zoster or polyoma viral infections, and certain antibiotics cross-react with tacrolimus.
  • Measuring serum creatinine is a simple test and it is the most commonly used indicator of renal function. A rise in blood creatinine levels is observed only with marked damage to functioning nephrons. Therefore, this test is not suitable for detecting early stage kidney disease. A better estimation of kidney function is given by the creatinine clearance test. Creatinine clearance can be accurately calculated using serum creatinine concentration and some or all of the following variables: sex, age, weight, and race as suggested by the American Diabetes Association without a 24 hour urine collection. Some laboratories will calculate the creatinine clearance if written on the pathology request form; and, the necessary age, sex, and weight are included in the subject information.
  • the subject is started on broad spectrum antibiotics until the culture results are known. If the condition worsens, and the culture reveals a specific infection, for example candida , a specific antifungal, fluconazole, can be administered to the known subject. However, this antifungal may alter the levels of the immunosuppressive agent given to almost all allogenic transplant recipients, tacrolimus. Upon testing for both tacrolimus and creatinine levels, the physician halts the tacrolimus, believing that the fluconazole will defeat the infection, and in a rapid manner. Under this regimen, the subject may worsen if the candida species is resistant to fluconazole, and the subject is then started on an appropriate anti-fungal agent.
  • candida a specific antifungal
  • fluconazole a specific antifungal
  • this antifungal may alter the levels of the immunosuppressive agent given to almost all allogenic transplant recipients, tacrolimus.
  • tacrolimus Upon testing for both tacrolimus and creatinine levels, the physician halts the tac
  • the tacrolimus may be halted, the immunosuppressive therapy is unmanaged and the subject may become unresponsive to any additional therapy and death may ensue. Thus, if there was a test to simultaneously monitor creatinine (kidney function), tacrolimus blood levels, and accurate identification of opportunistic infections, the above subject may have been saved.
  • the systems and methods of the invention can include a multiplexed, no sample preparation, single detection method, automated system to determine the drug level, the toxicity or adverse effect determinant, and the pathogen identification having a critical role in the immunocompromised subject setting.
  • a cartridge having portals or wells containing 1) magnetic particles having creatinine specific antibodies decorated on their surface, 2) magnetic particles having tacrolimus specific antibodies on their surface, and 3) magnetic particles having specific nucleic acid probes to identify pathogen species could be employed to rapidly determine and provide clinical management values for a given transplant subject.
  • Opportunistic infections that can be monitored in such subjects, and any other patient populations at risk of infection, include, without limitation, fungal; candida (resistant and non-resistant strains); gram negative bacterial infections (e.g., E. coli, stenotrophomonas maltophilia, Klebsiella pneumonia/oxytoca , or Pseudomonas aeruginosa ); and gram positive bacterial infections (e.g., Staphylococcus species: S. aureus, S. pneumonia, E. faecalis , and E. faecium ).
  • fungal fungal
  • candida resistant and non-resistant strains
  • gram negative bacterial infections e.g., E. coli, stenotrophomonas maltophilia, Klebsiella pneumonia/oxytoca , or Pseudomonas aeruginosa
  • gram positive bacterial infections e.g., Staphylococcus species: S
  • opportunistic infections that can be monitored include coaglulase negative staphylococcus, Corynebacterium spp., Fusobacterium spp., and Morganella morganii , and viral organisms, such as CMV, BKV, EBC, HIV, HCV, HBV, and HAV.
  • the systems and methods of the invention can also be used to monitor and diagnose cancer patients as part of a multiplexed diagnostic test.
  • One specific form of cancer, colorectal cancer has demonstrated positive promise for personalized medical treatment for a specific solid tumor.
  • Pharmacogenetic markers can be used to optimize treatment of colorectal and other cancers.
  • Significant individual genetic variation exists in drug metabolism of 5FU, capecitabine, irinotecan, and oxaliplatin that influences both the toxicity and efficacy of these agents.
  • Examples of genetic markers include UGT1A1*28 leads to reduced conjugation of SN-38, the active metabolite of irinotecan, resulting in an increased rate of adverse effects, especially neutropenia.
  • 5-FU toxicity is predicted by DPYD*2A.
  • Efficacy of oxaliplatin is influenced by polymorphisms in components of DNA repair systems, such as ERCC1 and XRCC1. Polymorphic changes in the endothelial growth factor receptor probably predict cetuximab efficacy.
  • the antibody-depended cell-mediated cytotoxic effect of cetuximab may be reduced by polymorphisms in the immunoglobin G fragment C receptors.
  • Polymorphic changes in the VEGF gene and the hypoxia inducible factor 1 alpha gene are also believed to play a role in the variability of therapy outcome.
  • identification of such polymorphisms in subjects can be used to assist physicians with treatment decisions.
  • PCR-based genetics tests have been developed to assist physicians with therapeutic treatment decisions for subjects with non-small cell lung cancer (NSCLC), colorectal cancer (CRC) and gastric cancer.
  • NSCLC non-small cell lung cancer
  • CRC colorectal cancer
  • gastric cancer gastric cancer.
  • Expression of ERCC1, TS, EGFR, RRM1, VEGFR2, HER2, and detection of mutations in KRAS, EGFR, and BRAF are available for physicians to order to identify the optimal therapeutic option.
  • these PCR tests are not available on site, and thus the sample must be delivered to the off-site laboratory.
  • FFPE Form-Fixed, Paraffin-Embedded (tissue) samples are prepared.
  • the systems and methods of the invention can be used without the 5-7 day turnaround to get the data and information and use of fixed samples required for existing methods.
  • the systems and methods of the invention can provide a single platform to analyze samples, without sample prep, for multiple analyte types, as in cancer for chemotherapeutic drugs, genpotyping, toxicity and efficacy markers can revolutionize the practice of personalized medicine and provide rapid, accurate diagnostic testing.
  • the systems and methods of the invention can also be used to monitor and diagnose neurological disease, such as dementia (a loss of cognitive ability in a previously-unimpaired person) and other forms of cognitive impairment.
  • dementia a loss of cognitive ability in a previously-unimpaired person
  • the short-term syndrome of delirium (often lasting days to weeks) can easily be confused with dementia, because they have all symptoms in common, save duration, and the fact that delirium is often associated with over-activity of the sympathetic nervous system.
  • Some mental illnesses, including depression and psychosis may also produce symptoms that must be differentiated from both delirium and dementia. Routine blood tests are also usually performed to rule out treatable causes.
  • Acetylcholinesterase inhibitors-Tacrine (Cognex), donepezil (Aricept), galantamine (Razadyne), and rivastigmine (Exelon) are approved by the United States Food and Drug Administration (FDA) for treatment of dementia induced by Alzheimer disease. They may be useful for other similar diseases causing dementia such as Parkinsons or vascular dementia.
  • N-methyl-D-aspartate blockers include memantine (Namenda), which is a drug representative of this class. It can be used in combination with acetylcholinesterase inhibitors.
  • Amyloid deposit inhibitors include minocycline and clioquinoline, which are antibiotics that may help reduce amyloid deposits in the brains of persons with Alzheimer disease.
  • Depression is frequently associated with dementia and generally worsens the degree of cognitive and behavioral impairment.
  • Antidepressants effectively treat the cognitive and behavioral symptoms of depression in subjects with Alzheimer's disease, but evidence for their use in other forms of dementia is weak. Many subjects with dementia experience anxiety symptoms.
  • benzodiazepines like diazepam (Valium) have been used for treating anxiety in other situations, they are often avoided because they may increase agitation in persons with dementia and are likely to worsen cognitive problems or are too sedating.
  • Buspirone (Buspar) is often initially tried for mild-to-moderate anxiety. There is little evidence for the effectiveness of benzodiazepines in dementia, whereas there is evidence for the effectiveness of antipsychotics (at low doses).
  • Selegiline a drug used primarily in the treatment of Parkinson's disease, appears to slow the development of dementia. Selegiline is thought to act as an antioxidant, preventing free radical damage. However, it also acts as a stimulant, making it difficult to determine whether the delay in onset of dementia symptoms is due to protection from free radicals or to the general elevation of brain activity from the stimulant effect. Both typical antipsychotics (such as haloperidol) and atypical antipsychotics such as (risperidone) increases the risk of death in dementia-associated psychosis. This means that any use of antipsychotic medication for dementia-associated psychosis is off-label and should only be considered after discussing the risks and benefits of treatment with these drugs, and after other treatment modalities have failed.
  • Dementia can be broadly categorized into two groups: cortical dementias and subcortical dementias.
  • Cortical dementias include: Alzheimer's disease, vascular dementia (also known as multi-infarct dementia), including Binswanger's disease, dementia with Lewy bodies (DLB), alcohol-induced persisting dementia, Korsakoff's syndrome, Wernicke's encephalopathy, frontotemporal lobar degenerations (FTLD), including Pick's disease, frontotemporal dementia (or frontal variant FTLD), semantic dementia (or temporal variant FTLD), progressive non-fluent aphasia, Creutzfeldt-Jakob disease, dementia pugilistica, Moyamoya disease, thebestia (often mistaken for a cancer), posterior cortical atrophy or Benson's syndrome.
  • vascular dementia also known as multi-infarct dementia
  • DLB dementia with Lewy bodies
  • FTLD frontotemporal lobar degenerations
  • Pick's disease frontotemporal dementia (or frontal variant FTLD), semantic dementia (or temporal variant FTLD)
  • Subcortical dementias include dementia due to Huntington's disease, dementia due to hypothyroidism, dementia due to Parkinson's disease, dementia due to vitamin B1 deficiency, dementia due to vitamin B12 deficiency, dementia due to folate deficiency, dementia due to syphilis, dementia due to subdural hematoma, dementia due to hypercalcaemia, dementia due to hypoglycemia, AIDS dementia complex, pseudodementia (a major depressive episode with prominent cognitive symptoms), aubstance-induced persisting dementia (related to psychoactive use and formerly absinthism), dementia due to multiple etiologies, fementia due to other general medical conditions (i.e., end stage renal failure, cardiovascular disease etc.), or dementia not otherwise specified (used in cases where no specific criteria is met).
  • dementia due to Huntington's disease dementia due to hypothyroidism
  • dementia due to Parkinson's disease dementia due to vitamin B1 deficiency
  • dementia due to vitamin B12 deficiency dementia due to folate
  • Alzheimer's disease is a common form of dementia.
  • the method of the invention can be a multiplexed, no sample preparation, single detection method, automated system to determine the drug level, the toxicity or adverse effect determinant, and the potential biomarker of the progression of the disease.
  • a cartridge having portals or wells containing 1) magnetic particles having protein biomarker specific antibodies decorated on their surface, 2) magnetic particles having specific antibodies on their surface, and 3) magnetic particles having nucleic acid specific probes to identify protein expression levels could be employed to rapidly determine and provide clinical management values for a given dementia subject.
  • the systems and methods of the invention can also be used to monitor and diagnose infectious disease in a multiplexed, automated, no sample preparation system.
  • pathogens that may be detected using the devices, systems, and methods of the invention include, e.g., Candida (resistant and non-resistant strains), e.g., C. albicans, C. glabrata, C. krusei, C. tropicalis , and C. parapsilosis; A. fumigatus; E. coli, Stenotrophomonas maltophilia, Klebsiella pneumonia/oxytoca, P. aeruginosa; Staphylococcus spp. (e.g., S. aureus or S. pneumonia ); E.
  • Candida resistant and non-resistant strains
  • C. albicans e.g., C. albicans, C. glabrata, C. krusei, C. tropicalis , and C. parapsilosis
  • the systems and methods of the invention can be used to identify and monitor the pathogenesis of disease in a subject, to select therapeutic interventions, and to monitor the effectiveness of the selected treatment.
  • the systems and methods of the invention can be used to identify the infectious virus, viral load, and to monitor white cell count and/or biomarkers indicative of the status of the infection.
  • the identity of the virus can be used to select an appropriate therapy.
  • the therapeutic intervention e.g., a particular antiviral agent
  • the systems and methods of the invention can be used to monitor a viral infection in a subject, e.g., with a viral panel configured to detect Cytomegalovirus (CMV), Epstein Barr Virus, BK Virus, Hepatitis B virus, Hepatitis C virus, Herpes simplex virus (HSV), HSV1, HSV2, Respiratory syncytial virus (RSV), Influenza; Influenza A, Influenza A subtype H1, Influenza A subtype H3, Influenza B, Human Herpes Virus 6, Human Herpes Virus 8, Human Metapneumovirus (hMPV), Rhinovirus, Parainfluenza 1, Parainfluenza 2, Parainfluenza 3, and Adenovirus.
  • CMV Cytomegalovirus
  • Epstein Barr Virus Epstein Barr Virus
  • BK Virus Hepatitis B virus
  • Hepatitis C virus Herpes simplex virus
  • Influenza Influenza
  • the methods of the invention can be used to monitor a suitable therapy for the subject with a viral infection (e.g., Abacavir, Aciclovir, Acyclovir, Adefovir, Amantadine, Amprenavir, Ampligen, Arbidol, Atazanavir, Atripla, Boceprevir, Cidofovir, Combivir, Darunavir, Delavirdine, Didanosine, Docosanol, Edoxudine, Efavirenz, Emtricitabine, Enfuvirtide, Entecavir, Famciclovir, Fomivirsen, Fosamprenavir, Foscarnet, Fosfonet, Ganciclovir, Ibacitabine, Immunovir, Idoxuridine, Imiquimod, Indinavir, Inosine, Integrase inhibitor, Interferon type III, Interferon type II, Interferon type I, Interferon ⁇ , Interferon ⁇ , Lamivudin
  • the systems and methods of the invention can also be used to monitor HIV/AIDS patients.
  • clinicians suspect acute infection e.g., in a subject with a report of recent risk behavior in association with symptoms and signs of the acute retroviral syndrome
  • a test for HIV RNA is usually performed.
  • High levels of HIV RNA detected in plasma through use of sensitive amplification assays (PCR, bDNA, or NASBA), in combination with a negative or indeterminate HIV antibody test support the diagnosis of acute HIV infection.
  • Low-level positive PCR results ( ⁇ 5000 copies/mL) are often not diagnostic of acute HIV infection and should be repeated to exclude a false-positive result.
  • HIV RNA levels tend to be very high in acute infection; however, a low value may represent any point on the upward or downward slope of the viremia associated with acute infection.
  • Plasma HIV RNA levels during seroconversion do not appear significantly different in subjects who have acute symptoms versus those who are asymptomatic. Viremia occurs approximately 2 weeks prior to the detection of a specific immune response.
  • Subjects diagnosed with acute HIV infection by HIV RNA. Fever and flu- or mono-like symptoms are common in acute HIV infection but are nonspecific rash, mucocutaneous ulcers, or pharyngeal candidiasis and meningismus are more specific and should raise the index of suspicion testing still require antibody testing with confirmatory Western blot 3 to 6 weeks later.
  • Subjects undergoing HIV testing who are not suspected to be in the acute stages of infection should receive HIV antibody testing according to standard protocol. Antibody test results that are initially negative should be followed up with HIV antibody testing at 3 months to identify HIV infection in individuals who may not yet have seroconverted at the time of initial presentation.
  • Plasma HIV RNA levels indicate the magnitude of HIV replication and its associated rate of CD4+ T cell destruction, while CD4+ T-cell counts indicate the extent of HIV-induced immune damage already suffered.
  • Regular, periodic measurement of plasma HIV RNA levels and CD4+ T-cell counts is necessary to determine the risk of disease progression in an HIV-infected individual and to determine when to initiate or modify antiretroviral treatment regimens.
  • AZT zidovudine
  • 3TC lamvudine
  • ABC abacavir
  • ATV atazanavir
  • d4T stavudine
  • ddI didanosine
  • NVP nevirapine
  • EFV efavirenz
  • FTC emtricitabine
  • LPV lopinavir
  • RTV ritonavir
  • TDF tenofovir disoproxil fumarate
  • Drug therapy for HIV is to commence in subjects who have a CD4 count ⁇ 350 cell/mm 3 irrespective of clinical symptoms. At least one of the four following regimens for antiretroviral na ⁇ ve subjects is begun: I) AZT+3TC+EFV, 2) AZT+3TC+NVP, 3) TDF+3TC or FTC+EFV, or 4) TDF+3TC or FTC+NVP. These regimens avoid d4T (stavudine) to limit the disfiguring, unpleasant, and potentially life-threatening toxicities of this drug. Treatment failure is usually determined by viral load, a persistent value of 5,000 copies/ml confirms treatment failure. In cases whereby viral load measurement is not available, immunological criteria (CD4 cell count) can be used to determine therapeutic progress.
  • CD4 cell count can be used to determine therapeutic progress.
  • a boosted protease inhibitor plus two nucleoside analogs are added to the regimen and is considered second line antiretroviral therapy.
  • ATV plus low dose RTV, or LPV with low dose RTV is also considered second line therapy.
  • the goal in treatment failure cases is simpler timed regimens and fixed doses.
  • Each of the antiretroviral drugs used in combination therapy regimens should always be used according to optimum schedules and dosages.
  • the available effective antiretroviral drugs are limited in number and mechanism of action, and cross-resistance between specific drugs has been documented. Therefore, any change in antiretroviral therapy increases future therapeutic constraints.
  • the systems and methods of the invention can be used in a multiplexed, no sample preparation, single detection method, automated system to determine the drug level, the toxicity or adverse effect determinants, and the potential biomarker of the progression of the disease.
  • a cartridge having portals or wells containing 1) magnetic particles having CD4 cell specific antibodies decorated on their surface, 2) magnetic particles having toxicity biomarker specific antibodies on their surface, and 3) magnetic particles having nucleic acid specific probes to identify viral load levels could be employed to rapidly determine and provide clinical management values for a given HIV/AIDS subject.
  • the systems and methods of the invention can also be used to monitor and diagnose immune disease in a subject (e.g., Crohn's disease, ileitis, enteritis, inflammatory bowel disease, irritable bowel syndrome, ulcerative colitis, as well as non-gastrointestinal immune disease).
  • a subject e.g., Crohn's disease, ileitis, enteritis, inflammatory bowel disease, irritable bowel syndrome, ulcerative colitis, as well as non-gastrointestinal immune disease.
  • Remicade also known as Infliximab, an anti-TNF antibody
  • these agents are expensive and at least one-third of the eligible patients fail to show any useful response. Finding a means to predict those who will respond, and to anticipate relapse is, therefore, of obvious importance.
  • T helper-type 1 (Th1) lymphocytes orchestrate much of the inflammation in Crohn's disease mainly via production of TNF-alpha, which appears to play a pivotal role as a pro-inflammatory cytokine. It exerts its effects through its own family of receptors (TNFR1 and TNFR2), the end results of which include apoptosis, c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) activation and NF-kappaB activation. Activated NF-kappaB enters the nucleus and induces transcription of genes associated with inflammation, host defense and cell survival.
  • TNFR1 and TNFR2 family of receptors
  • JNK/SAPK c-Jun N-terminal kinase/stress-activated protein kinase
  • NF-kappaB Activated NF-kappaB enters the nucleus and induces transcription of genes associated with inflammation, host defense
  • the promoter region of the TNF gene lies between nucleotides ⁇ 1 and ⁇ 1300, and encompasses numerous polymorphic sites associated with potential binding sites for various transcription factors.
  • Carriers of the TNF allele 2 (TNF2) (which contains a single base-pair polymorphism at the ⁇ 308 promoter position) produce slightly more TNF-alpha in their intestinal mucosa than non-TNF2 carriers.
  • TNF polymorphisms also appear to influence the nature and frequency of extra-intestinal manifestations of inflammatory bowel disease (IBD).
  • IBD inflammatory bowel disease
  • the method of the invention can be a multiplexed, no sample preparation, single detection method, automated system to determine the drug level, the toxicity or adverse effect determinants, and the potential biomarker of the progression of the disease.
  • a cartridge having portals or wells containing 1) magnetic particles having anti-TNF-alpha specific antibodies decorated on their surface, 2) magnetic particles having toxicity biomarker specific antibodies on their surface, and 3) magnetic particles having specific probes to identify disease markers of progression could be employed to rapidly determine and provide clinical management values for a given Crohn's disease patient.
  • the systems and methods of the invention can also be used to monitor and diagnose infectious disease and inflammation in a multiplexed, automated, no sample preparation system.
  • Such systems and methods could be used to monitor, for example, bacteremia, sepsis, and/or Systemic Inflammatory Response Syndrome (SIRS).
  • SIRS Systemic Inflammatory Response Syndrome
  • Early diagnosis is clinically important as this type of infection, if left untreated, can lead to organ dysfunction, hypoperfusion, hypotension, refractory (septic) shock/SIRS shock, and/or Multiple Organ Dysfunction Syndrome (MODS).
  • MODS Multiple Organ Dysfunction Syndrome
  • HAI healthcare-associated infections
  • hospital-acquired or hospital-onset infections are most commonly caused by viral, bacterial, and fungal pathogens and are commonly transmitted via wounds, invasive devices (catheters, tracheostomy, intubation, surgical drains) or ventilators and are found as urinary tract infections, surgical site infections, or a form of pneumonia.
  • invasive devices catheters, tracheostomy, intubation, surgical drains
  • ventilators are found as urinary tract infections, surgical site infections, or a form of pneumonia.
  • a patient's flora begins to acquire characteristics of the surrounding bacterial pool.
  • Risk factors for the development of catheter-associated bloodstream infections in neonates include catheter hub colonization, exit site colonization, catheter insertion after the first week of life, duration of parenteral nutrition, and extremely low birth weight ( ⁇ 1000 g) at the time of catheter insertion.
  • catheter-associated bloodstream infections increase with neutropenia, prolonged catheter dwell time (>7 days), use of percutaneously placed CVL (higher than tunneled or implanted devices), and frequent manipulation of lines.
  • Candida infections are increasingly important pathogens in the NICU.
  • Risk factors for the development of candidemia in neonates include gestational age less than 32 weeks, 5-min Apgar scores of less than 5, shock, disseminated intravascular coagulopathy, prior use of intralipids, parenteral nutrition administration, CVL use, 1-12 blocker administration, intubation, or length of stay longer than 7 days.
  • Risk factors for the development of ventilator-associated pneumonia (VAP) in pediatric patients include reintubation, genetic syndromes, immunodeficiency, and immunosuppression. In neonates, a prior episode of bloodstream infection is a risk factor for the development of VAP.
  • Risk factors for the development of healthcare-associated urinary tract infection in pediatric patients include bladder catheterization, prior antibiotic therapy, and cerebral palsy.
  • MRSA Metal-resistant Staphylococcus aureus
  • gram-positive bacteria gram-positive bacteria
  • Helicobacter which is gram-negative.
  • antibiotic drugs that can treat diseases caused by Gram-positive MRSA
  • Acinetobacter there are currently few effective drugs for Acinetobacter .
  • Common pathogens in bloodstream infections are coagulase-negative staphylococci, Enterococcus , and Staphylococcus aureus .
  • Candida albicans and pathogens for pneumonia such as Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae , and Haemophilus influenza account for many infections.
  • Pathogens for urinary tract infections include Escherichia coli, Candida albicans , and Pseudomonnas aeruginosa .
  • Gram-negative enteric organisms are additionally common in urinary tract infections.
  • Surgical site infections include Staphylococcus aureus, Pseudomonas aeruginosa , and coagulase-negative staphylococci.
  • the infectious agent can be selected from, without limitation, pathogens associated with sepsis, such as Acinetobacter baumannii, Aspergillus fumigatis, Bacteroides fragilis, B.
  • MRSA Mec A gene
  • Morganella morgana Neisseria meningitidis, Neisseria spp. non- meningitidis, Prevotella buccae, P. intermedia, P. melaminogenica, Propionibacterium acnes, Proteus mirabilis, P. vulgaris, Pseudomonas aeruginosa, Salmonella enterica, Serratia marcescens, Staphylococcus aureus, S. haemolyticus, S. maltophilia, S. saprophyticus, Stenotrophomonas maltophilia, S.
  • the method and system will be designed to ascertain whether the infectious agent bears a Van A gene or Van B gene characteristic of vancomycin resistance; mecA for methicillin resistance, NDM-1 and ESBL for more general resistance to beta-lactams.
  • Sepsis or septic shock are serious medical conditions that are characterized by a whole-body inflammatory state (systemic inflammatory response syndrome or SIRS) and the presence of a known or suspected infection.
  • Sepsis is defined as SIRS in the presence of an infection
  • septic shock is defined as sepsis with refractory arterial hypotension or hypoperfusion abnormalities in spite of adequate fluid resuscitation
  • severe sepsis is defined as sepsis with organ dysfunction, hypoperfusion, or hypotension.
  • sepsis is characterized by presence of acute inflammation present throughout the entire body, and is, therefore, frequently associated with fever and leukocytosis or low white blood cell count and lower-than-average temperature, and vomiting.
  • SIRS sepsis is the host's immune response to an infection and it is thought that this response causes most of the symptoms of sepsis, resulting in hemodynamic consequences and damage to organs.
  • SIRS is characterized by hemodynamic compromise and resultant metabolic derangement. Outward physical symptoms of this response frequently include a high heart rate (above 90 beats per minute), high respiratory rate (above 20 breaths per minute), elevated WBC count (above 12,000) and elevated or lowered body temperature (under 36° C. (97° F.) or over 38° C. (100° F.)).
  • Sepsis is differentiated from SIRS by the presence of a known pathogen. For example, SIRS and a positive blood culture for a pathogen indicates the presence of sepsis.
  • SIRS sepsis
  • HMBG-1 High mobility group-box 1 protein
  • IL-1 receptor IL-1 receptor antagonist
  • IL-1b IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18
  • MIP-1 macrophage inflammatory protein
  • MIF macrophage migration inhibitory factor
  • osteopontin RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5)
  • TNF- ⁇ TNF- ⁇
  • C-reactive protein C-reactive protein
  • CD64 monocyte chemotactic protein 1
  • the systems and methods can be designed to monitor certain proteins characteristic of sepsis, such as adenosine deaminase binding protein (ABP-26), inducible nitric oxide synthetase (iNOS), lipopolysaccharide binding protein (LBP), and procalcitonin (PCT).
  • Sepsis is usually treated in the intensive care unit with intravenous fluids and antibiotics. If fluid replacement is insufficient to maintain blood pressure, specific vasopressor medications can be used. Mechanical ventilation and dialysis may be needed to support the function of the lungs and kidneys, respectively.
  • a central venous catheter and an arterial catheter may be placed.
  • Sepsis patients may require preventive measures for deep vein thrombosis, stress ulcers and pressure ulcers, and some patients may benefit from tight control of blood sugar levels with insulin (targeting stress hyperglycemia), low-dose corticosteroids, or activated drotrecogin alfa (recombinant protein C).
  • insulin targeting stress hyperglycemia
  • low-dose corticosteroids or activated drotrecogin alfa (recombinant protein C).
  • activated drotrecogin alfa recombinant protein C
  • methods and systems of the invention provide a diagnostic platform for the rapid identification of one or more pathogens, and whether or not the pathogens are resistant to certain therapies (for the selection of an appropriate antimicrobial therapy).
  • the platform as described allows for the simultaneous determination of the levels of the factors (e.g., GRO-alpha, High mobility group-box 1 protein (HMBG-1), IL-1 receptor, IL-1 receptor antagonist, IL-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, macrophage inflammatory protein (MIP-1), macrophage migration inhibitory factor (MIF), osteopontin, RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5), TNF- ⁇ , C-reactive protein (CRP), CD64, and monocyte chemotactic protein 1 (MCP-1)) and/or proteins (e.g., adenosine deaminase binding protein (ABP-26), inducible nitric oxide synthetase (iNOS), lipopolysaccharide binding protein (LBP), and procalcitonin (PCT)) thought to be involved in SIRS,
  • this platform reduces the empirical protocols and/or use of non-specific/general antimicrobials that may or may not be targeting the specific pathogen and/or the underlying system dysfunction for a given patient.
  • This platform allows for rapid and accurate diagnoses, which can point to effective therapy, providing a key component to a physician's decision making and reducing morbidity and mortality.
  • Another method to distinguish symptomatic patients for instance, patients with systemic inflammatory syndrome, or SIRS, from septic patients, is to use biomarkers that correlate either individually or via an index, to identify patients with infection.
  • these biomarkers which can be multiple types of analytes (cytokines, metabolites, DNA, RNA/gene expression, etc.) will indicate infection and thus sepsis.
  • one panel could be: (i) gram positiive clusters (e.g., S. aureus , and CoNS (coagulase negative staph)); (ii) gram positive chains/pairs (e.g., Strep spp., mitis, pneumonia spp., agalactiae spp., pyogenes spp., Enterococcus spp. ( E. faecium, E. fetalis ); (iii) gram negative rods (e.g., E.
  • This panel should be used in conjunction with a fungal assay for full coverage.
  • the categories represent the information required for an effective intervention with appropriate therapy, given that each site of care will have an empirically derived approach based on a positive response to gram +, gram ⁇ , etc.
  • the species identified in each category represent those that would fit under each heading, but are not comprehensive. Further, a pan-bacterial marker is included to cover any species that is not covered by the diagnostic method employed for each category. Further, the combination of results will also give an indication of the species, although not fully, if included as described above. Cross-referencing positives and negatives by category allow a process of elimination approach to identify some of the species, probabilistically.
  • IL-1 ⁇ High mobility group-box 1 protein
  • HMBG-1 High mobility group-box 1 protein
  • IL-1 receptor IL-1 receptor antagonist
  • IL-1b High mobility group-box 1 protein
  • IL-1b IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18
  • MIP-1 macrophage inflammatory protein
  • MIF macrophage migration inhibitory factor
  • osteopontin RANTES (regulated on activation, normal T-cell expressed and secreted; or CCL5)
  • IL-10 GM-CSF
  • MCP-1 TNF- ⁇
  • hsCRP hsCRP
  • PCT normal T-cell expressed and secreted
  • lactate lactate
  • Cardiac markers or cardiac enzymes are proteins that leak out of injured myocardial cells and are used to assess cardiac injury.
  • Cardiac markers include, without limitation, the enzymes SGOT, LDH, the MB subtype of the enzyme creatine kinase, and cardiac troponins (T and I).
  • the cardiac troponins T and I which are released within 4-6 hours of an attack of myocardial infarction (and remain elevated for up to 2 weeks) have nearly complete tissue specificity and are now the preferred markers for assessing myocardial damage.
  • Elevated troponins in the setting of chest pain may accurately predict a high likelihood of a myocardial infarction in the near future.
  • the diagnosis of myocardial infarction is typically based upon subject history, ECG, and cardiac markers. When damage to the heart occurs, levels of cardiac markers rise over time, which is why blood tests for them are taken over a 24-hour period. Because these enzyme levels are not elevated immediately following a heart attack, patients presenting with chest pain are generally treated with the assumption that a myocardial infarction has occurred and then evaluated for a more precise diagnosis.
  • a MI is a medical emergency which requires immediate medical attention. Treatment attempts to salvage as much myocardium as possible and to prevent further complications, thus the phrase “time is muscle”.
  • Oxygen, aspirin, and nitroglycerin are usually administered as soon as possible.
  • monitoring Troponin I and T, as well as potential other biomarkers of cardiac ischemia, in addition to drug therapy and toxicity patterns in a single platform diagnostic method would have distinct advantages.
  • the systems and methods of the invention can be used to provide a multiplexed, no sample preparation, single detection method, automated system to determine the drug level, the toxicity or adverse effect determinants, and the potential biomarker of the progression of the disease.
  • a cartridge having portals or wells containing 1) magnetic particles having anti-troponin I or troponin T specific antibodies decorated on their surface, 2) magnetic particles having toxicity biomarker specific antibodies on their surface, and 3) magnetic particles having specific probes to identify disease markers of progression could be employed to rapidly determine and provide clinical management values for a given myocardial infarction patient.
  • One or more multi-well cartridges can be configured for use in the systems and methods of the invention and prepared with at least one whole blood sample from the patient; magnetic particles for detecting each of the analytes to be detected (one or more small molecules; one or more metabolites of the one or more small molecules; metabolic biomarker such as described for the hepatic function panel); and dilution and wash buffers.
  • Liver function tests are done on a patient's serum or plasma sample and clinical biochemistry laboratory blood analysis furnishes crucial data regarding the condition of the patient's liver.
  • a “hepatic function panel” is a blood test wherein low or high levels of one or more enzymes may point to liver diseases or damage.
  • the hepatic function panel can include one or more of the following analyte detection assays: one or more small molecules; one or more metabolites of the one or more small molecules; a biologic, metabolic biomarkers; genotyping, gene expression profiling; and proteomic analysis.
  • a hepatic function panel can include analysis of one or more of the following proteins in a patient or subject biological sample: 1) albumin (the major constituent of the total protein in the liver; while the remnant is called globulin; albumin must be present as 3.9 to 5.0 g/dL, hypoalbuminaemia indicates poor nutrition, lower protein catabolism, cirrhosis or nephrotic syndrome); 2) aspartate transaminase (AST) (also known as serum glutamic oxaloacetic transaminase or aspartate aminotransferase, is an enzyme in liver parenchymal cells and is normally 10 to 34 IU/L; elevated levels are indicative of acute liver damage); 3) alanine transaminase (ALT) (also known as serum glutamic pyruvic transaminase or alanine aminotransferase, is an enzyme is present in hepatocytes at levels between 8 to 37 IU/L; elevated levels are indicative of acute liver damage in viral hepatitis
  • An additional hepatic function panel may include genotyping of cytochrome P450 enzymes.
  • the cytochrome P450 superfamily (CYP) is a large and diverse group of enzymes. The function of most CYP enzymes is to catalyze the oxidation of organic substances.
  • the substrates of CYP enzymes include metabolic intermediates such as lipids and steroidal hormones, as well as xenobiotic substances such as drugs and other toxic chemicals.
  • CYPs are the major enzymes involved in drug metabolism and bioactivation, accounting for ca. 75% of the total metabolism. Most drugs undergo biotransformation and are eventually excreted from the body; and many require bioactivation to form the active compound.
  • the CYP enzymes that metabolize many medications include CYP3A4/5 (36%), CYP2D6 (19%), CYP2C8/9 (16%), and CYP1A2 (11%).
  • Cytochrome P450 genotyping tests are used to determine how well a patient or subject metabolizes a drug.
  • the results of cytochrome P450 tests can be used to divide individuals into four main types:
  • cytochrome P450 status in a patient sample can be accomplished by measuring the enzyme activity of the sample, or determining if a genetic difference occurs in one of the genes of this metabolic system in the genome. Genotyping requires a cell sample representative of the patient or subject's genome and the analysis is aimed at determining genetic differences in these clinically important genes.
  • CYP450 enzyme phenotyping (identifying enzymatic metabolizer status) can be accomplished by administering a test enzyme substrate to a patient and monitoring parent substrate and metabolite concentrations over time (e.g., in urine).
  • testing and interpretation are time-consuming and inconvenient; as a result, phenotyping is seldom performed.
  • CYP2C19 metabolizes several important types of drugs, including proton-pump inhibitors, diazepam, propranolol, imipramine, and amitriptyline.
  • a hepatic function panel employing the methods of the invention, may be used to genotype patient or subject samples to assess the status of the cytochrome P450 enzyme system to then optimize therapeutic efficacy and safety.
  • CYP2D6 cytochrome P450 2D6
  • SSRI selective serotonin reuptake inhibitors
  • TCA tricylic antidepressants
  • beta-blockers such as Inderal
  • Type 1A antiarrhythmics Approximately 10% of the population has a slow acting form of this enzyme and 7% a super-fast acting form. Thirty-five percent are carriers of a non-functional 2D6 allele, especially elevating the risk of ADRs when these individuals are taking multiple drugs.
  • Drugs that CYP2D6 metabolizes include Prozac, Zoloft, Paxil, Effexor, hydrocodone, amitriptyline, Claritin, cyclobenzaprine, Haldol, metoprolol, Rythmol, Tagamet, tamoxifen, dextromethorphan, beta-blockers, antiarrhythmics, antidepressants, and morphine derivatives, including many of the most prescribed drugs and the over-the-counter diphenylhydramine drugs (e.g., Allegra, Dytuss, and Tusstat).
  • CYP2D6 is responsible for activating the pro-drug codeine into its active form and the drug is therefore inactive in CYP2D6 slow metabolizers.
  • CYP2C9 cytochrome P450 2C9 is the primary route of metabolism for Coumadin (warfarin). Approximately 10% of the population are carriers of at least one allele for the slow-metabolizing form of CYP2C9 and may be treatable with 50% of the dose at which normal metabolizers are treated.
  • Other drugs metabolized by CYP2C9 include Amaryl, isoniazid, ibuprofen, amitriptyline, Dilantin, Hyzaar, THC (tetrahydrocannabinol), naproxen, and Viagra.
  • CYP2C19 cytochrome P450 2C19 is associated with the metabolism of carisoprodol, diazepam, Dilantin, and Prevacid.
  • CYP1A2 (cytochrome P450 1A2) is associated with the metabolism of amitriptyline, olanzapine, haloperidol, duloxetine, propranolol, theophylline, caffeine, diazepam, chlordiazepoxide, estrogens, tamoxifen, and cyclobenzaprine.
  • NAT2 N-acetyltransferase 2 is a secondary drug metabolizing enzyme that acts on isoniazid, procainamide, and Azulfidine.
  • the frequency of the NAT2 “slow acetylator” in various worldwide populations ranges from 10% to more than 90%.
  • DPD Dihydropyrimidine dehydrogenase
  • Fluorouracil 5-FU
  • UGT1A1 UDP-glucuronosyltransferase variations can lead to severe even fatal reactions to the first dost of Camptosar (irinotecan).
  • 5HTT Serotonin Transporter
  • 5HTT Serotonin Transporter helps determine whether people are likely to respond to SSRIs, a class of medications that includes citalopram, fluoxetine, paroxetine, and sertraline, among others, and often is prescribed for depression or anxiety.
  • the AmpliChip® (Roche Molecular Systems, Inc.) is the only FDA-cleared test for CYP450 genotyping.
  • the AmpliChip® is a microarray consisting of many DNA sequences complementary to 2 CYP450 genes and applied in microscopic quantities at ordered locations on a solid surface (chip).
  • the AmpliChip® tests the DNA from a patient's white blood cells collected in a standard anticoagulated blood sample for 29 polymorphisms and mutations for the CYP2D6 gene and 2 polymorphisms for the CYP2C19 gene.
  • the invention features a multiplexed analysis of a single blood sample (e.g., a single blood draw, or any other type of patient sample described herein) from a patient to determine a) liver enzymatic status, as well as b) the genotype of key metabolic enzymes to then be able to design pharmacotherapy regimes for optimal therapeutic care using the systems and methods of the invention.
  • a single blood sample e.g., a single blood draw, or any other type of patient sample described herein
  • the systems and methods of the invention can include one or more multi-well cartridges prepared with at least one whole blood sample from the patient; magnetic particles for detecting each of the analytes to be detected; analyte antibodies; multivalent binding agents; and/or dilution and wash buffers for use in a multiplexed assay as described above.
  • Renal toxicity is a common side effect of use of xenobiotics and early, rapid detection of early stages of nephrotoxicity may assist in medical decision making.
  • Early reports of detection of renal toxicity suggest that increased mRNA expression of certain genes can be monitored.
  • markers of renal toxicity can be detected in urine. These markers include: kim-1, lipocalin-2, neutrophil gelatinase-associated lipocalin (NGAL), timp-1, clusterin, osteopontin, vimentin, and heme oxygenase 1 (HO-1). More broadly, detection of DNA, heavy metal ions or BUN levels in urine can be useful clinical information.
  • the methods and utlity of the instant invention also includes the ability to detect these markers of renal toxicity.
  • a hepatic function panel may also include one or two hallmark biomarkers of nephrotoxicity, or visa versa.
  • the magnetic particles described herein may be utilized in an assay that does not feature particle agglomeration.
  • the magnetic particles may be used to capture or concentrate an analyte, e.g., by passing a liquid sample containing the analyte over magnetic particles that include binding moieties specific for the analyte.
  • Some advantages of this approach include a) no clusters need be formed (the clusters may be inherently unstable over a certain size, leading to increased CV's); b) no clustering may not require vortexing as flow shear forces may dislodge non-specific binding of magnetic particles, c) fluidic handling steps may be reduced, and d) miniaturization of the assay may favor these non-agglomerative methods.
  • two models for surface based detection include: (i) changes in T2 signal arising from the depletion of magnetic particles from a solution and (ii) changes in T2 signal arising from magnetic particle enrichment of a surface.
  • the magnetic particles derivatized with a binding moiety can be held in position by an external magnetic field while sample containing the corresponding analyte is circulated past the “trapped” magnetic particles allowing for capture and/or concentrate the analyte of interest.
  • the particles may be pulled to the side or bottom of the assay vessel, or a magnetizable mesh or magnetizable metal foam with appropriate pore size can be present in the reaction vessel, creating very high local magnetic gradients.
  • An advantage of having the mesh/metal foam in the reaction vessel is that the distance each magnetic particle needs to travel to be “trapped” or “captured” can be very short, improving assay kinetics.
  • Another non-agglomerative assay is to have surfaces derivitized with ligands complementary to the binding moiety present on the magnetic particle and using a capture/depletion/flow through format. Specific binding of magnetic particles to a surface depletes magnetic particles from the bulk particle suspension used in the assay, thus leading to a change in the T 2 value in the reaction volume interrogated by the MR reader. Pre-incubation of the particles with the sample containing analyte can reduce/inhibit the specific binding/capture/depletion of the magnetic particle by the derivitized surface in proportion to the concentration of analyte in the sample.
  • This type of assay approach has been demonstrated using PhyNexus affinity chromatography micropipette tips.
  • the 200 ul PhyTips contain a 20 ⁇ l volume of resin bed trapped between 2 fits.
  • the resin bed consists of 200 ⁇ m cross-linked agarose beads derivitized with avidin, protein A, protein G, or an analyte.
  • a programmable electronic pipettor can aspirate and dispense various volumes at various flow rates.
  • the magnetic particles flow through the pores created by the packed agarose bead resin bed.
  • the amount of particle depletion can be quantified.
  • Another non-agglomerative assay format is similar to that described above, but uses derivatized magnetizable metal foam to replace the resin bed.
  • the advantage of the metal foam as the solid phase substrate is that when placed in a magnetic field, the metal foam generates very high local magnetic field gradients over very short distances which can attract the derivatized magnetic particles and bring them in contact with the complementary binding partner on the metal foam and improve the chances of a specific productive interaction.
  • the assay kinetics can be vastly improved because the particles need to travel much shorter distances to find a complementary surface to bind.
  • the particle concentration in the flow-through reaction volume will be reduced inversely proportional to the analyte concentration in the sample and can be quantified using the MR reader.
  • the metal foam can be nickel bearing directly bound his-tagged moieties, or can be nickel treated with aminosilane and covalently linkedbinding moieties. This process has been demonstrated using aminosilane-treated nickel metal foam with 400 ⁇ m pores decorated with anti-creatinine antibodies and shown to specifically bind creatinine-derivatized magnetic particles.
  • NMF material is incubated with deionized water and then frozen.
  • the frozen water in the NMF crevices support the foam so that it will not collapse or create differential edges.
  • a punch is used to create uniform-sized pieces of NMF;
  • a hammer and punch e.g., a circular tube having a circular cutting edge at one end
  • a wire is then used to poke out the pieces, which are dried in a glassware oven.
  • NMF pieces are cleaned with 2M H 2 S0 4 in a sonicator, and sulfuric acid solution is used to clean the NMF and to roughen the NMF surfaces in order to assist in subsequent attachment of the amino groups of aminosilane.
  • the acid-washed NMF pieces are then rinsed with deionized water to remove any residual acid solution, and the NMF pieces are dried in a glassware oven.
  • the NMF pieces are derivatized with aminosilane, and 70 kD aminodextran is covalently attached.
  • the aminodextran is then optionally crosslinked with gluteraldehyde.
  • Specific antibodies, oligonucleotides, and analytes can then be covalently attached to the amino groups on the aminodextran using various chemistries, and the derivatized NMF pieces are incubated to block non-specific binding.
  • Common blockers include but are not limited to BSA, non-fat dried milk, detergents, salmon sperm DNA, among others.
  • assays that would be aimed at detecting a physical property change in a liquid sample.
  • PCT/US2009/062537 published as WO2010/051362
  • PCT/US2008/073346 published as WO2009/026164
  • coagulation of blood can be determined by the instant methods described therein.
  • other physical properties may be detected such as solidification, changes in density and may have uses in determining curing of materials (plastic compositions), changes in food and food products with time, contamination of products found in nature, and monitoring certain biological fluids such as urine as a function of kidney function.
  • the magnetic particles utilized in the non-agglomerative methods described herein can have an average diameter of from 10 nm to 1200 nm (e.g., from 10 to 50, 50 to 150, 150 to 250, 200 to 350, 250 to 450, 300 to 500, 450 to 650, 500 to 700 nm, 700 to 850, 800 to 950, 900 to 1050, or from 1000 to 1200 nm).
  • Systems and methods of the invention can include amplification based nucleic acid detection assays conducted starting with complex samples (e.g., for diagnostic, forensic, and environmental analyses).
  • Sample preparation must also remove or provide resistance for common PCR inhibitors found in complex samples (e.g., body fluids, soil, or other complex milieu). Common inhibitors are listed in Table 5 (see also, Wilson, Appl. Environ. Microbiol., 63:3741 (1997)). Inhibitors typically act by either prevention of cell lysis, degradation or sequestering a target nucleic acid, and/or inhibition of a polymerase activity. The most commonly employed polymerase, Taq, is inhibited by the presence of 0.1% blood in a reaction.
  • mutant Taq polymerases have been engineered that are resistant to common inhibitors (e.g., hemoglobin and/or humic acid) found in blood and soil (Kermekchiev et al., Nucl. Acid. Res., 37(5): e40, (2009)). Manufacturer recommendations indicate these mutations enable direct amplification from up to 20% blood. Despite resistance afforded by the mutations, accurate real time PCR detection is complicated due to fluorescence quenching observed in the presence of blood sample (Kermekchiev et al., Nucl. Acid. Res., 37:e40 (2009)).
  • common inhibitors e.g., hemoglobin and/or humic acid
  • Substrate Target Inhibitor feces Escherichia coli >10 ⁇ circumflex over ( ) ⁇ 3 bacterial cells ion-exchange column CSF Treponema Cellular debris causing nested primers pallidum nonspecific amplification whole blood mammalian >4 ⁇ l of blood/100-ml reaction 1-2% blood per reaction tissue mix (hemoglobin) feces Rotatvirus unknown dilution cellulose fiber clinical Cytomegalovirus unidentified components glass bead extraction specimens human blood human genes DNA binding proteins thermophilic protease and tissue from Thermus strain rt44A mammalian Mammalian thermal cycler variations formamide tissue tissue genetics mammalian Mammalian thermal cycler variations DMSO, glycerol, PEG, tissue tissue genetics organic solvents clinical Treponema unknown factors Various substrate-specific specimens pallidum physicochemical methods forensic Sper
  • Polymerase chain reaction amplification of DNA or cDNA is a tried and trusted methodology; however, as discussed above, polymerases are inhibited by agents contained in crude samples, including but not limited to commonly used anticoagulants and hemoglobin. Recently mutant Taq polymerases have been engineered to harbor resistance to common inhibitors found in blood and soil.
  • polymerases e.g., HemoKlenTaqTM (New England BioLabs, Inc., Ipswich, Mass.) as well as OmniTaqTM and OmniKlenTaqTM (DNA Polymerase Technology, Inc., St.
  • Taq polymerase that render them capable of amplifying DNA in the presence of up to 10%, 20% or 25% whole blood, depending on the product and reaction conditions (See, e.g., Kermekchiev et al. Nucl. Acids Res. 31:6139 (2003); and Kermekchiev et al., Nucl. Acid. Res., 37:e40 (2009); and see U.S. Pat. No. 7,462,475).
  • Phusion® Blood Direct PCR Kits include a unique fusion DNA polymerase enzyme engineered to incorporate a double-stranded DNA binding domain, which allows amplification under conditions which are typically inhibitory to conventional polymerases such as Taq or Pfu, and allow for amplification of DNA in the presence of up to about 40% whole blood under certain reaction conditions. See Wang et al., Nuc. Acids Res. 32:1197 (2004); and see U.S. Pat. Nos. 5,352,778 and 5,500,363.
  • Kapa Blood PCR Mixes provide a genetically engineered DNA polymerase enzyme which allows for direct amplification of whole blood at up to about 20% of the reaction volume under certain reaction conditions.
  • direct optical detection of generated amplicons is not possible with existing methods since fluorescence, absorbance, and other light based methods yield signals that are quenched by the presence of blood. See Kermekchiev et al., Nucl. Acid. Res., 37:e40 (2009).
  • complex samples such as whole blood can be directly amplified using about 5%, about 10%, about 20%, about 25%, about 30%, about 25%, about 40%, and about 45% or more whole blood in amplification reactions, and that the resulting amplicons can be directly detected from amplification reaction using magnetic resonance (MR) relaxation measurements upon the addition of conjugated magnetic particles bound to oligonucleotides complementary to the target nucleic acid sequence.
  • the magnetic particles can be added to the sample prior to amplification.
  • direct detection of hybridized magnetic particle conjugates and amplicons is via MR relaxation measurements (e.g., T 2 , T 1 , T1/T2 hybrid, T 2 *, etc).
  • MR relaxation measurements e.g., T 2 , T 1 , T1/T2 hybrid, T 2 *, etc.
  • methods which are kinetic, in order to quantify the original nucleic acid copy number within the sample e.g., sampling and nucleic acid detection at pre-defined cycle numbers, comparison of endogenous internal control nucleic acid, use of exogenous spiked homologous competitive control nucleic acid).
  • amplification or “amplify” or derivatives thereof as used herein mean one or more methods known in the art for copying a target or template nucleic acid, thereby increasing the number of copies of a selected nucleic acid sequence.
  • Amplification may be exponential or linear.
  • a target or template nucleic acid may be either DNA or RNA.
  • the sequences amplified in this manner form an “amplified region” or “amplicon.”
  • Primer probes can be readily designed by those skilled in the art to target a specific template nucleic acid sequence. In certain preferred embodiments, resulting amplicons are short to allow for rapid cycling and generation of copies.
  • the size of the amplicon can vary as needed to provide the ability to discriminate target nucleic acids from non-target nucleic acids.
  • amplicons can be less than about 1,000 nucleotides in length. Desirably the amplicons are from 100 to 500 nucleotides in length (e.g., 100 to 200, 150 to 250, 300 to 400, 350 to 450, or 400 to 500 nucleotides in length).
  • PCR polymerase chain reaction
  • numerous other methods are known in the art for amplification of nucleic acids (e.g., isothermal methods, rolling circle methods, etc.). Those skilled in the art will understand that these other methods may be used either in place of, or together with, PCR methods. See, e.g., Saiki, “Amplification of Genomic DNA” in PCR Protocols, Innis et al., Eds., Academic Press, San Diego, Calif., pp 13-20 (1990); Wharam et al., Nucleic Acids Res. 29:E54 (2001); Hafner et al., Biotechniques, 30:852 (2001).
  • PCR polymerase chain reaction
  • RT-PCR reverse transcription PCR
  • LCR transcription based amplification system
  • TAS transcription mediated amplification
  • NASBA transcription mediated amplification
  • SDA strand displacement amplification
  • LAMP loop mediated isothermal amplification
  • ICAN isothermal and chimeric primer-initiated amplification of nucleic acid
  • SMAP smart amplification system
  • PCR process is disclosed in U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188, each of which is incorporated herein by reference.
  • One set of primers complementary to a template DNA are designed, and a region flanked by the primers is amplified by DNA polymerase in a reaction including multiple amplification cycles.
  • Each amplification cycle includes an initial denaturation, and up to 50 cycles of annealing, strand elongation (or extension) and strand separation (denaturation).
  • the DNA sequence between the primers is copied.
  • Primers can bind to the copied DNA as well as the original template sequence, so the total number of copies increases exponentially with time.
  • PCR can be performed as according to Whelan, et al, Journal of Clinical Microbiology, 33:556 (1995).
  • Various modified PCR methods are available and well known in the art.
  • Various modifications such as the “RT-PCR” method, in which DNA is synthesized from RNA using a reverse transcriptase before performing PCR; and the “TaqMan PCR” method, in which only a specific allele is amplified and detected using a fluorescently labeled TaqMan probe, and Taq DNA polymerase, are known to those skilled in the art.
  • RT-PCR and variations thereof have been described, for example, in U.S. Pat. Nos.
  • LCR is a method of DNA amplification similar to PCR, except that it uses four primers instead of two and uses the enzyme ligase to ligate or join two segments of DNA. Amplification can be performed in a thermal cycler (e.g., LCx of Abbott Labs, North Chicago, Ill.). LCR can be performed for example, as according to Moore et al., Journal of Clinical Microbiology 36:1028 (1998). LCR methods and variations have been described, for example, in European Patent Application Publication No. EP0320308, and U.S. Pat. No. 5,427,930, each of which is incorporated herein by reference.
  • the TAS method is a method for specifically amplifying a target RNA in which a transcript is obtained from a template RNA by a cDNA synthesis step and an RNA transcription step.
  • a sequence recognized by a DNA-dependent RNA polymerase i.e., a polymerase-binding sequence or PBS
  • PBS polymerase-binding sequence
  • an RNA polymerase is used to synthesize multiple copies of RNA from the cDNA template.
  • Amplification using TAS requires only a few cycles because DNA-dependent RNA transcription can result in 10-1000 copies for each copy of cDNA template.
  • TAS can be performed according to Kwoh et al., PNAS 86:1173 (1989).
  • the TAS method has been described, for example, in International Patent Application Publication No. WO1988/010315, which is incorporated herein by reference.
  • Transcription mediated amplification is a transcription-based isothermal amplification reaction that uses RNA transcription by RNA polymerase and DNA transcription by reverse transcriptase to produce an RNA amplicon from target nucleic acid.
  • TMA methods are advantageous in that they can produce 100 to 1000 copies of amplicon per amplification cycle, as opposed to PCR or LCR methods that produce only 2 copies per cycle.
  • TMA has been described, for example, in U.S. Pat. No. 5,399,491 which is incorporated herein by reference.
  • NASBA is a transcription-based method which for specifically amplifying a target RNA from either an RNA or DNA template.
  • NASBA is a method used for the continuous amplification of nucleic acids in a single mixture at one temperature.
  • a transcript is obtained from a template RNA by a DNA-dependent RNA polymerase using a forward primer having a sequence identical to a target RNA and a reverse primer having a sequence complementary to the target RNA a on the 3′ side and a promoter sequence that recognizes T7 RNA polymerase on the 5′ side.
  • a transcript is further synthesized using the obtained transcript as template. This method can be performed as according to Heim, et al., Nucleic Acids Res., 26:2250 (1998).
  • the NASBA method has been described in U.S. Pat. No. 5,130,238, which is incorporated herein by reference.
  • the SDA method is an isothermal nucleic acid amplification method in which target DNA is amplified using a DNA strand substituted with a strand synthesized by a strand substitution type DNA polymerase lacking 5′ ⁇ 3′ exonuclease activity by a single stranded nick generated by a restriction enzyme as a template of the next replication.
  • a primer containing a restriction site is annealed to template, and then amplification primers are annealed to 5′ adjacent sequences (forming a nick).
  • Amplification is initiated at a fixed temperature. Newly synthesized DNA strands are nicked by a restriction enzyme and the polymerase amplification begins again, displacing the newly synthesized strands.
  • SDA can be performed according to Walker, et al., PNAS, 89:392 (1992). SDA methods have been described in U.S. Pat. Nos. 5,455,166 and 5,457,027, each of which are incorporated by reference.
  • the LAMP method is an isothermal amplification method in which a loop is always formed at the 3′ end of a synthesized DNA, primers are annealed within the loop, and specific amplification of the target DNA is performed isothermally.
  • LAMP can be performed according to Nagamine et al., Clinical Chemistry. 47:1742 (2001). LAMP methods have been described in U.S. Pat. Nos. 6,410,278; 6,974,670; and 7,175,985, each of which are incorporated by reference.
  • the ICAN method is anisothermal amplification method in which specific amplification of a target DNA is performed isothermally by a strand substitution reaction, a template exchange reaction, and a nick introduction reaction, using a chimeric primer including RNA-DNA and DNA polymerase having a strand substitution activity and RNase H.
  • ICAN can be performed according to Mukai et al., J. Biochem. 142: 273 (2007).
  • the ICAN method has been described in U.S. Pat. No. 6,951,722, which is incorporated herein by reference.
  • the SMAP (MITANI) method is a method in which a target nucleic acid is continuously synthesized under isothermal conditions using a primer set including two kinds of primers and DNA or RNA as a template.
  • the first primer included in the primer set includes, in the 3′ end region thereof, a sequence (Ac′) hybridizable with a sequence (A) in the 3′ end region of a target nucleic acid sequence as well as, on the 5′ side of the above-mentioned sequence (Ac′), a sequence (B′) hybridizable with a sequence (Bc) complementary to a sequence (B) existing on the 5′ side of the above-mentioned sequence (A) in the above-mentioned target nucleic acid sequence.
  • the second primer includes, in the 3′ end region thereof, a sequence (Cc′) hybridizable with a sequence (C) in the 3′ end region of a sequence complementary to the above-mentioned target nucleic acid sequence as well as a loopback sequence (D-Dc′) including two nucleic acid sequences hybridizable with each other on an identical strand on the 5′ side of the above-mentioned sequence (Cc′).
  • SMAP can be performed according to Mitani et al., Nat. Methods, 4(3): 257 (2007). SMAP methods have been described in U.S. Patent Application Publication Nos. 2006/0160084, 2007/0190531 and 2009/0042197, each of which is incorporated herein by reference.
  • the amplification reaction can be designed to produce a specific type of amplified product, such as nucleic acids that are double stranded; single stranded; double stranded with 3′ or 5′ overhangs; or double stranded with chemical ligands on the 5′ and 3′ ends.
  • the amplified PCR product can be detected by: (i) hybridization of the amplified product to magnetic particle bound complementary oligonucleotides, where two different oligonucleotides are used that hybridize to the amplified product such that the nucleic acid serves as an interparticle tether promoting particle agglomeration; (ii) hybridization mediated detection where the DNA of the amplified product must first be denatured; (iii) hybridization mediated detection where the particles hybridize to 5′ and 3′ overhangs of the amplified product; (iv) binding of the particles to the chemical or biochemical ligandson the termini of the amplified product, such as streptavidin functionalized particles binding to biotin functionalized amplified product.
  • the systems and methods of the invention can be used to perform real time PCR and provide quantitative information about the amount of target nucleic acid present in a sample (see FIG. 52 and Example 18).
  • Methods for conducting quantitative real time PCR are provided in the literature (see for example: RT-PCR Protocols. Methods in Molecular Biology, Vol. 193. Joe O'Connell, ed. Totowa, N.J.: Humana Press, 2002, 378 pp. ISBN 0-89603-875-0.).
  • Example 18 describes use of the methods of the invention for real time PCR analysis of a whole blood sample.
  • the systems and methods of the invention can be used to perform real time PCR directly in opaque samples, such as whole blood, using magnetic nanoparticles modified with capture probes and magnetic separation.
  • Using real-time PCR allows for the quantification of a target nucleic acid without opening the reaction tube after the PCR reaction has commenced.
  • biotin or avidin labeled primers can be used to perform real-time PCR. These labels would have corresponding binding moieties on the magnetic particles that could have very fast binding times. This allows for a double stranded product to be generated and allows for much faster particle binding times, decreasing the overall turnaround time.
  • the binding chemistry would be reversible, preventing the primers from remaining particle bound.
  • the sample can be heated or the pH adjusted.
  • the real-time PCR can be accomplished through the generation of duplex DNA with overhangs that can hybridize to the superparamagnetic particles.
  • LNA and/or fluorinated capture probes may speed up the hybridization times.
  • Pan Candida F 5′-CAT GAT CTG CTG CAG /iSp18/GG Uni-Tail CAT GCC TGT TTG AGC GTC-3′ Pan Candida R 5′-GCA GAA CTC CAG ACC /iSp18/GC Uni-Tail TTA TTG ATA TGC TTA AGT TCA GCG GGT-3′ (SEQ ID NO. 20) 3′AM universal 5′-CTG CAG CAG ATC ATG TTT tail CP TTT TTT TTT /3AmM0/-3′ (SEQ ID NO.
  • the particles are designed to have a hairpin that buries the binding site to the amplicon. Heating the particles to a higher melt temperature would expose the binding site of the hairpin to allow binding to the target.
  • a probe that hybridizes to an amplicon is tethering two (or more) particles.
  • the reaction would be conducted in the presence of a polymerase with 5′ exonuclease activity, resulting in the cleavage of the inter-particle tether and a subsequent change in T2.
  • the polymerase is selected to have exonuclease activity and compatibility with the matrix of choice (e.g. blood).
  • smaller particles e.g., 30 nm CLIO
  • can be used to reduce steric hindrance of the hybridization to target or subsequent enzymatic digestion during polymerization see, e.g., Heid et al Genome Research 1996 6: 986-994).
  • two particle populations can be synthesized to bear complementary capture probes.
  • the capture probes hybridize promoting particle clustering.
  • the amplicon can compete, hybridize, and displace the capture probes leading to particle declustering.
  • the method can be conducted in the presence or absence of nanoparticles. The particles free in solution will cluster and decluster due to the thermocycling (because, e.g., the Tm can be below 95° C.).
  • the Tm of the amplicon binding to one of the particle-immobilized capture probes can be designed such that that binding interaction is more favorable than the particle-to-particle binding interaction (by, e.g., engineering point mutations within the capture probes to thermodynamically destabilize the duplexes).
  • the particle concentration can be kept at, e.g., low or high levels. Examples of probes and primers useful in such a system are set forth in the table below.
  • the invention features the use of enzymes compatible with whole blood, e.g., NEB Hemoklentaq, DNAP Omniklentaq, Kapa Biosystems whole blood enzyme, Thermo-Fisher Finnzymes Phusion enzyme.
  • enzymes compatible with whole blood e.g., NEB Hemoklentaq, DNAP Omniklentaq, Kapa Biosystems whole blood enzyme, Thermo-Fisher Finnzymes Phusion enzyme.
  • the invention also features quantitative asymmetric PCR.
  • the method can involve the following steps:
  • a variety of impurities and components of whole blood can be inhibitory to the polymerase and primer annealing. These inhibitors can lead to generation of false positives and low sensitivities.
  • it is desirable to utilize a thermal stable polymerase not inhibited by whole blood samples see, e.g., U.S. Pat. No. 7,462,475) and include one or more internal PCR assay controls (see Rosenstraus et al. J. Clin Microbiol. 36:191 (1998) and Hoofar et al., J. Clin. Microbiol. 42:1863 (2004)).
  • the assay can include an internal control nucleic acid that contains primer binding regions identical to those of the target sequence.
  • the target nucleic acid and internal control can be selected such that each has a unique probe binding region that differentiates the internal control from the target nucleic acid.
  • the internal control is, optionally, employed in combination with a processing positive control, a processing negative control, and a reagent control for the safe and accurate determination and identification of an infecting organism in, e.g., a whole blood clinical sample.
  • the internal control can be an inhibition control that is designed to co-amplify with the nucleic acid target being detected.
  • the assays of the invention can include one or more positive processing controls in which one or more target nucleic acids is included in the assay (e.g., each included with one or more cartridges) at 3 ⁇ to 5 ⁇ the limit of detection.
  • the measured T2 for each of the positive processing controls must be above the pre-determined threshold indicating the presence of the target nucleic acid.
  • the positive processing controls can detect all reagent failures in each step of the process (e.g., lysis, PCR, and T2 detection), and can be used for quality control of the system.
  • the assays of the invention can include one or more negative processing controls consisting of a solution free of target nucleic acid (e.g., buffer alone).
  • the T2 measurements for the negative processing control should be below the threshold indicating a negative result while the T2 measured for the internal control is above the decision threshold indicating an internal control positive result.
  • the purpose of the negative control is to detect carry-over contamination and/or reagent contamination.
  • the assays of the invention can include one or more reagent controls.
  • the reagent control will detect reagent failures in the PCR stage of the reaction (i.e. incomplete transfer of master mix to the PCR tubes).
  • the reagent controls can also detect gross failures in reagent transfer prior to T2 detection.
  • PCR PCR-like plasmid clones derived from organisms that have been previously analyzed and that may be present in larger numbers in the laboratory environment, and c) repeated amplification of the same target sequence leading to accumulation of amplification products in the laboratory environment.
  • a common source of the accumulation of the PCR amplicon is aerosolization of the product. Typically, if uncontrolled aerosolization occurs, the amplicon will contaminate laboratory reagents, equipment, and ventilation systems.
  • a positive sample may contain 250 ng PCR product in 50 ⁇ l. This gives a total of 3.9 1011 copies of a 600 bp double-stranded product. One thousandth of a microliter of this reaction will contain approximately 8 million copies. If a very small and invisible aerosol is formed when the PCR vessel is opened, there is a possibility that this aerosol can contain a very large number of amplified products. Furthermore, the microscopic droplets in an aerosol are able to float for a long time in the air, and if there is turbulence in the room, they can be carried a long way. Considering the fact that only one copy is enough to create a false positive reaction, it is obvious that great care must be taken to avoid this carry-over contamination.
  • Sample preparation workstations can be cleaned (e.g., with 10% sodium hypochlorite solution, followed by removal of the bleach with ethanol). Oxidative breakdown of nucleic acids prevents reamplification of impurities in subsequent PCR reactions.
  • Sterilization of the amplification products ensures that subsequent diagnostic assays are not compromised by carryover DNA, and must follow two generally accepted criteria: (a) the PCR needs to be exposed to the environment after there has been some form of modification of amplicon, and (b) the modification must not interfere with the detection method.
  • UV irradiation can effectively remove contaminating DNA (see Rys et al., J. Clin Microbiol. 3:2356 (1993); and Sarker et al., Nature, 343:27 (1990)), but the irradiation of the PCR reagents must take place before addition of polymerase, primers, and template DNA.
  • UV light sterilization of the amplification products uses the property of UV light to induce thymine dimmers and other covalent modifications of the DNA that render the contaminating DNA un-amplifiable.
  • incorporation of dUTP into the amplified fragments will also alter the composition of the product so that it is different from the template DNA composition (see Longo et al., Gene 93:125 (1990); and U.S. Pat. Nos. 5,035,996; 7,687,247; and 5,418,149).
  • the enzyme Uracil-N-Glycosylase (UNG) is added together with the normal PCR enzyme to the reaction mix.
  • the UNG enzyme will cleave the uracil base from DNA strands before amplification, and leave all the old amplified products unable to act as templates for new amplification, but will not react on unincorporated dUTP or new template. This will efficiently remove contaminating PCR products from the reaction after the PCR vessel has been closed, and thus no new contamination is possible.
  • the use of dUTP in PCR reactions to prevent carry-over can cause problems when the products are used in a later hybridization study, due to the low capability of uracil to act in hybridization (Carmody et al., Biotechniques 15:692 (1993)).
  • dUTP is incorporated instead of dTTP.
  • a later hybridization signal with the probe may be eliminated.
  • the probe binding site should be chosen with no more than 25% T's, and without stretches of poly-T.
  • the PCR should contain equal concentrations of dUTP and dTTP and not only dUTP.
  • the increase in product amplification when using dUTP especially when AT-rich target sequences are selected. This is probably because the incorporation of dUTP decreases re-annealing of formed PCR products which would prevent primers from annealing.
  • the primer binding sites should be selected with a low content of T's, since primer annealing also will be inhibited by dUTP incorporation (Carmody et al., Biotechniques 15:692 (1993)).
  • Heat labile UDG isolated from BMTU 3346 is described in Schmidt et al. Biochemica 2:13 (1996) (see also U.S. Pat. No. 6,187,575).
  • a uracil-DNA glycosylase gene from Psychrobacter sp HJ147 was described in U.S. Pat. No. 7,723,093.
  • Lastly a cod uracil-DNA glycosylase was described (U.S. Pat. No. 7,037,703).
  • DNase digestion after PCR can be used to reduce contamination.
  • a heat labile DNase enzyme was identified that can be used to digest ds DNA to remove any contaminating DNA prior to the PCR amplification step of the target DNA.
  • the ds DNA is digested, the sample is heated to inactivate the DNase, and the target sample and PCR reactants are added to the reaction tube to carry out the target specific PCR. (see U.S. Pat. No. 6,541,204).
  • Sterilization after PCR can be used to reduce contamination. Incorporation of a photochemical reagent (isopsoralen) into the product during amplification will create a difference in composition between the template DNA and the amplified PCR products (see Rys et al., J. Clin Microbiol. 3:2356 (1993)). Furocoumarin compounds, such as isopsoralen or psoralen, are a class of planar tricylcic reagents that are known to intercalate between base pairs of nucleic acids (see U.S. Pat. No. 5,532,145). Light treatment of the closed PCR vessel will render previously formed PCR products unable to act as templates for further amplification.
  • primer hydrolysis can be used to sterilize a reaction after amplification.
  • Primer hydrolysis of sterilization of amplification products relies on the uniquely synthesized chimeric primers that contain one or more ribose linkages at the 3′ end.
  • the generated amplification products containing those ribose residues are susceptible to alkaline hydrolysis at the site of the ribose molecule.
  • the method includes exposure to 1M NaOH and incubated for 30 minutes to hydrolyze the amplification products at the sites of the incorporated ribose.
  • the old amplicon has lost its primer site due to the hydrolysis of the ribose molecules and the new amplicon will have the primer binding sites.
  • addition of hydroxylamine hydrochloride to PCR reaction tubes after amplification sterilizes the reaction contents, and is especially effective for short ( ⁇ 100 bp) and GC rich amplification products.
  • the hydroxylamine preferentially reacts with oxygen atoms in the cytosine residues and creates covalent adducts that prevent base-pairing with guanine residues in subsequent reactions.
  • the modified amplification product are not recognized as amplification targets in subsequent PCR reactions.
  • One or more of the methods described above can be used in conjunction with the methods of the invention to reduce the risk of contamination and false positives. Carry-over of old amplified PCR products can be a very serious risk in the nucleic acid analysis in the T2 Biosystems diagnostic platform. One way to prevent this contamination is to physically divide the PCR working areas. Alternatives to the physical separation of the PCR reaction method include UV irradiation of PCR mix and incorporation of reagents into the newly formed PCR product can be used to alter it from the template.
  • the reaction of magnetic particles and specific analytes to form aggregates can be used to produce a diagnostic signal in the assays of the invention. In many instances, incubation of the reaction mixture for a period of time is sufficient to form the aggregates.
  • the methods, kits, cartridges, and devices of the invention can be configured to shorten the amount of time needed to capture a particular analyte, or produce aggregates of magnetic particles.
  • the kinetics of aggregation can be increased by passing the particle/analyte solution through a vessal in which there is a narrowing of the path of the fluid flow.
  • the narrowing enhances particle-particle interactions.
  • the aggregation of magnetic particles can be accelerated by applying an acoustic standing wave to the sample (see Aboobaker et al., Journal of Environmental Engineering, 129:427 (2003) and U.S. Pat. No. 4,523,682).
  • a flow chamber with two transducers at opposite ends can be used to generate an acoustic standing wave in the sample that causes the magnetic particles to migrate (or be segregated) in a manner that increases the rate of magnetic particle aggregation.
  • the aggregation of magnetic particles can be accelerated by applying an ultrasonic wave to the sample (see Masudo et al., Anal. Chem. 73:3467 (2001)).
  • ultrasound wave particles can move to the node of the wave along the ultrasound force gradient. This approach can be used to provide a reliable method for assisting the agglomeration reaction.
  • the aggregation of magnetic particles can be accelerated by electrostatic interactions. Electrostatic separation or movement of the magnetic particles utilizes inherent differences in friction charge characteristics, electric conductivity, and dielectric constants. Since the magnetic particles will behave differently under the application of an electrostatic field, movement and enhanced collisions can occur. Electrostatic force exertion on the particles can be proportional to the surface area available for surface charge, so the nanoparticles will typically move in the presence of the electrostatic field when coated with varying materials, such as dextran or other large molecular coatings, and whether or not the nanoparticle has bound to one of the binding moieties a analyte. The nanoparticles must first be charged and the charge could optionally be pulsed. See, for example, Sinyagin et al., J.
  • the magnetic particles derivatized with a binding moiety can be held in position by an external magnetic field while sample containing the corresponding analyte is circulated past the “trapped” magnetic particles allowing for capture and/or concentrate the analyte of interest.
  • the capture and/or aggregation can be facilitated by exposure to a magnetic field (i.e., MAA or gMAA) as described herein.
  • the kinetics of magnetic particle aggregation can be increased by sequestering the magnetic particles in a compartment defined by a porous membrane, such as a tea bag, that permits flow of analytes into and out of the compartment.
  • a porous membrane such as a tea bag
  • the increase in the local concentration of magnetic particles can increase the reaction kinetics between magnetic particles and analytes, and the kinetics of aggregation. After mixing the solution and magnetic particles for a predetermined period of time, the magnetic particles are released from the compartment and the sample is measured.
  • the particles may be pulled to the side or bottom of the assay vessel, or a magnetizable mesh or magnetizable metal foam with appropriate pore size can be present in the reaction vessel, creating very high local magnetic gradients.
  • the metal foam generates very high local magnetic field gradients over very short distances which can attract the derivatized magnetic particles and bring them in contact with the complementary binding partner on the metal foam and improve the chances of a specific productive interaction.
  • An advantage of having the mesh/metal foam in the reaction vessel is that the distance each magnetic particle needs to travel to be “trapped” or “captured” can be very short, improving assay kinetics.
  • a magnetizable mesh foam having pores of 100 to 1000 microns, a liquid sample, and magnetic particles for detecting an analyte in the liquid sample.
  • the reaction tube is exposed to a magnetic field to magnetize the mesh.
  • the magnetic particles are then attracted to the magnetized mesh and become trapped within the pores of the mesh.
  • the concentration of the magnetic particles within the mesh increases the reaction kinetics between the magnetic particles and the analyte diffusing into and out of the mesh (the reaction tube is optionally agitated to expedite the diffusion of analyte onto the trapped magnetic particles).
  • the mesh is then demagnetized (e.g., by heating the mesh or exposing the mesh to an alternating magnetic field), thereby permitting the release of magnetic particles complexed to analyte. Larger aggregates of magnetic particles can then be formed, completing the reaction.
  • the kinetics of magnetic particle aggregation can be increased by centrifugally pulling the magnetic particles down to the bottom of the sample tube.
  • the increase in the local concentration of magnetic particles can increase the aggregation kinetics.
  • the particles are, desirably, greater than about 30 nm in diameter.
  • FIG. 1A is a schematic diagram 100 of an NMR system for detection of a signal response of a liquid sample to an appropriate RF pulse sequence.
  • a bias magnet 102 establishes a bias magnetic field Bb 104 through a sample 106 .
  • the magnetic particles are in a liquid or lyophilized state in the cartridge prior to their introduction to a sample well (the term “well” as used herein includes any indentation, vessel, container, or support) 108 until introduction of the liquid sample 106 into the well 108 , or the magnetic particles can be added to the sample 106 prior to introduction of the liquid sample into the well 108 .
  • An RF coil 110 and RF oscillator 112 provides an RF excitation at the Larmor frequency which is a linear function of the bias magnetic field Bb.
  • the RF coil 110 is wrapped around the sample well 108 .
  • the excitation RF creates a nonequilibrium distribution in the spin of the water protons (or free protons in a non-aqueous solvent).
  • the protons When the RF excitation is turned off, the protons “relax” to their original state and emit an RF signal that can be used to extract information about the presence and concentration of the analyte.
  • the coil 110 acts as an RF antenna and detects a signal, which based on the applied RF pulse sequence, probes different properties of the material, for example a T 2 relaxation.
  • the signal of interest for some cases of the technology is the spin-spin relaxation (generally 10-2000 milliseconds) and is called the T 2 relaxation.
  • the RF signal from the coil 110 is amplified 114 and processed to determine the T 2 (decay time) response to the excitation in the bias field Bb.
  • the well 108 may be a small capillary or other tube with nanoliters to microliters of the sample, including the analyte and an appropriately sized coil wound around it (see FIG. 1B ). The coil is typically wrapped around the sample and sized according to the sample volume.
  • a solenoid coil about 50 mm in length and 10 to 20 mm in diameter could be used; for a sample having a volume of about 40 ⁇ l, a solenoid coil about 6 to 7 mm in length and 3.5 to 4 mm in diameter could be used; and for a sample having a volume of about 0.1 nl a solenoid coil about 20 ⁇ m in length and about 10 ⁇ m in diameter could be used.
  • the coil may be configured as shown in any of FIGS. 2A-2E about or in proximity to the well.
  • An NMR system may also contain multiple RF coils for the detection of multiplexing purposes.
  • the RF coil has a conical shape with the dimensions 6 mm ⁇ 6 mm ⁇ 2 mm.
  • FIGS. 2A-2E illustrate exemplary micro NMR coil (RF coil) designs.
  • FIG. 2A shows a wound solenoid micro coil 200 about 100 ⁇ m in length, however one could envision a coil having 200 ⁇ m, 500 ⁇ m or up to 1000 ⁇ m in length.
  • FIG. 2B shows a “planar” coil 202 (the coil is not truly planar, since the coil has finite thickness) about 1000 ⁇ m in diameter.
  • FIG. 2C shows a MEMS solenoid coil 204 defining a volume of about 0.02 ⁇ L.
  • FIG. 2D shows a schematic of a MEMS Helmholz coil 206 configuration
  • FIG. 2E shows a schematic of a saddle coil 220 configuration.
  • a wound solenoid micro coil 200 used for traditional NMR detection is described in Seeber et al., “Design and testing of high sensitivity micro-receiver coil apparatus for nuclear magnetic resonance and imaging,” Ohio State University, Columbus, Ohio.
  • a planar micro coil 202 used for traditional NMR detection is described in Massin et al., “High Q factor RF planar microcoil for micro-scale NMR spectroscopy,” Sensors and Actuators A 97-98, 280-288 (2002).
  • a Helmholtz coil configuration 206 features a well 208 for holding a sample, a top Si layer 210 , a bottom Si layer 212 , and deposited metal coils 214 .
  • Helmholtz coil configuration 206 used for traditional NMR detection is described in Syms et al, “MEMS Helmholz Coils for Magnetic Resonance Spectroscopy,” Journal of Micromechanics and Micromachining 15 (2005) S1-S9.
  • the NMR unit includes a magnet (i.e., a superconducting magnet, an electromagnet, or a permanent magnet).
  • the magnet design can be open or partially closed, ranging from U- or C-shaped magnets, to magnets with three and four posts, to fully enclosed magnets with small openings for sample placement.
  • the tradeoff is accessibility to the “sweet spot” of the magnet and mechanical stability (mechanical stability can be an issue where high field homogeneity is desired).
  • the NMR unit can include one or more permanent magnets, cylindrically shaped and made from SmCo, NdFeB, or other low field permanent magnets that provide a magnetic field in the range of about 0.5 to about 1.5 T (i.e., suitable SmCo and NdFeB permanent magnets are available from Neomax, Osaka, Japan).
  • suitable SmCo and NdFeB permanent magnets are available from Neomax, Osaka, Japan.
  • such permanent magnets can be a dipole/box permanent magnet (PM) assembly, or a hallbach design (See Demas et al., Concepts Magn Reson Part A 34A:48 (2009)).
  • the NMR units can include, without limitation, a permanent magnet of about 0.5 T strength with a field homogeneity of about 20-30 ppm and a sweet spot of 40 ⁇ L, centered.
  • This field homogeneity allows a less expensive magnet to be used (less tine fine-tuning the assembly/shimming), in a system less prone to fluctuations (e.g. temperature drift, mechanical stability over time-practically any impact is much too small to be seen), tolerating movement of ferromagnetic or conducting objects in the stray field (these have less of an impact, hence less shielding is needed), without compromising the assay measurements (relaxation measurements and correlation measurements do not require a highly homogeneous field).
  • the coil configuration may be chosen or adapted for specific implementation of the micro-NMR-MRS technology, since different coil configurations offer different performance characteristics. For example, each of these coil geometries has a different performance and field alignment.
  • the planar coil 202 has an RF field perpendicular to the plane of the coil.
  • the solenoid coil 200 has an RF field down the axis of the coil, and the Helmholtz coil 206 has an RF field transverse to the two rectangular coils 214 .
  • the Helmholtz 206 and saddle coils 220 have transverse fields which would allow the placement of the permanent magnet bias field above and below the well. Helmholtz 206 and saddle coils 220 may be most effective for the chip design, while the solenoid coil 200 may be most effective when the sample and MRS magnetic particles are held in a micro tube.
  • the micro-NMR devices may be fabricated by winding or printing the coils or by microelectromechanical system (MEMS) semiconductor fabrication techniques.
  • MEMS microelectromechanical system
  • a wound or printed coil/sample well module may be about 100 ⁇ m in diameter, or as large as a centimeter or more.
  • a MEMS unit or chip (thusly named since it is fabricated in a semiconductor process as a die on a wafer) may have a coil that is from about 10 ⁇ m to about 1000 ⁇ m in characteristic dimension, for example.
  • the wound or printed coil/sample well configuration is referenced herein as a module and the MEMS version is referenced herein as a chip.
  • the liquid sample 108 may be held in a tube (for example, a capillary, pipette, or micro tube) with the coil wound around it, or it may be held in wells on the chip with the RF coil surrounding the well.
  • the sample is positioned to flow through a tube, capillary, or cavity in the proximity to the RF coil.
  • the basic components of an NMR unit include electrical components, such as a tuned RF circuit within a magnetic field, including an MR sensor, receiver and transmitter electronics that could be including preamplifiers, amplifiers and protection circuits, data acquisitions components, pulse programmer and pulse generator.
  • Systems containing NMR units with RF coils and micro wells containing magnetic particle sensors described herein may be designed for detection and/or concentration measurement of specific analyte(s) of interest by development of a model for particle aggregation phenomena and by development of an RF-NMR signal chain model.
  • experiments can be conducted for analyte/magnetic particle systems of interest by characterizing the physics of particle aggregation, including, for example, the effects of affinities, relevant dimensions, and concentrations.
  • experiments can be conducted to characterize the NMR signal(s) (T 2 , T 1 , T 2 *, T 2rho , T 1rho and/or other signal characteristics, such as T1/T2 hybrid signals and may also include but are not limited to diffusion, susceptibility, frequency) as functions of particle aggregation or depletion and magnetic particle characteristics.
  • Signal characteristics specific to the MRS (magnetic resonance switch) phenomenon in a given system can be used to enhance detection sensitivity and/or otherwise improve performance.
  • the NMR system may include a chip with RF coil(s) and electronics micromachined thereon.
  • the chip may be surface micromachined, such that structures are built on top of a substrate. Where the structures are built on top of the substrate and not inside it, the properties of the substrate are not as important as in bulk micromachining, and expensive silicon wafers used in bulk micromachining can be replaced by less expensive materials such as glass or plastic.
  • Alternative embodiments, however, may include chips that are bulk micromachined.
  • Surface micromachining generally starts with a wafer or other substrate and grows layers on top. These layers are selectively etched by photolithography and either a wet etch involving an acid or a dry etch involving an ionized gas, or plasma. Dry etching can combine chemical etching with physical etching, or ion bombardment of the material. Surface micromachining may involve as many layers as is needed.
  • an inexpensive RF coil maybe integrated into a disposable cartridge and be a disposable component.
  • the coil could be placed in a manner that allows electrical contact with circuitry on the fixed NMR setup, or the coupling could be made inductively to a circuit.
  • the relaxation measurement is T 2
  • accuracy and repeatability will be a function of temperature stability of the sample as relevant to the calibration, the stability of the assay, the signal-to-noise ratio (S/N), the pulse sequence for refocusing (e.g., CPMG, BIRD, Tango, and the like), as well as signal processing factors, such as signal conditioning (e.g., amplification, rectification, and/or digitization of the echo signals), time/frequency domain transformation, and signal processing algorithms used.
  • Signal-to-noise ratio is a function of the magnetic bias field (Bb), sample volume, filling factor, coil geometry, coil Q-factor, electronics bandwidth, amplifier noise, and temperature.
  • NMR units for use in the systems and methods of the invention can be those described in U.S. Pat. No. 7,564,245, incorporated herein by reference.
  • the NMR units of the invention can include a small probehead for use in a portable magnetic resonance relaxometer as described in PCT Publication No. WO09/061,481, incorporated herein by reference.
  • the systems of the invention can be implantable or partially implantable in a subject.
  • the NMR units of the invention can include implantable radiofrequency coils and optionally implantable magnets as described in PCT Publication Nos. WO09/085214 and WO08/057578, each of which is incorporated herein by reference.
  • the systems of the invention can include a polymeric sample container for reducing, partly or completely, the contribution of the NMR signal associated with the sample container to the nuclear magnetic resonance parameter of the liquid sample as described in PCT Publication No. WO09/045354, incorporated herein by reference.
  • the systems of the invention can include a disposable sample holder for use with the MR reader that is configured to permit a predetermined number of measurements (i.e., is designed for a limited number of uses).
  • the disposable sample holder can include none, part, or all, of the elements of the RF detection coil (i.e., such that the MR reader lacks a detection coil).
  • the disposable sample holder can include a “read” coil for RF detection that is inductively coupled to a “pickup” coil present in the MR reader. When the sample container is inside the MR reader it is in close proximity to the pickup coil and can be used to measure NMR signal.
  • the disposable sample holder includes an RF coil for RF detection that is electrically connected to the MR reader upon insertion of the sample container.
  • the appropriate electrical connection is established to allow for detection.
  • the number of uses available to each disposable sample holder can be controlled by disabling a fusable link included either in the electrical circuit within the disposable sample holder, or between the disposable sample holder and the MR reader. After the disposable sample holder is used to detect an NMR relaxation in a sample, the instrument can be configure to apply excess current to the fusable link, causing the link to break and rendering the coil inoperable.
  • multiple fusable links could be used, working in parallel, each connecting to a pickup on the system, and each broken individually at each use until all are broken and the disposable sample holder rendered inoperable.
  • the systems for carrying out the methods of the invention can include one or more cartridge units to provide a convenient method for placing all of the assay reagents and consumables onto the system.
  • the system may be customized to perform a specific function, or adapted to perform more than one function, e.g., via changeable cartridge units containing arrays of micro wells with customized magnetic particles contained therein.
  • the system can include a replaceable and/or interchangeable cartridge containing an array of wells pre-loaded with magnetic particles, and designed for detection and/or concentration measurement of a particular analyte.
  • the system may be usable with different cartridges, each designed for detection and/or concentration measurements of different analytes, or configured with separate cartridge modules for reagent and detection for a given assay.
  • the cartridge may be sized to facilitate insertion into and ejection from a housing for the preparation of a liquid sample which is transferred to other units in the system (i.e., a magnetic assisted agglomeration unit, or an NMR unit).
  • the cartridge unit itself could potentially interface directly with manipulation stations as well as with the MR reader(s).
  • the cartridge unit can be a modular cartridge having an inlet module that can be sterilized independent of the reagent module.
  • An inlet module for sample aliquoting can be designed to interface with uncapped vacutainer tubes, and to aliquot two a sample volume that can be used to perform, for example, a candida assay (see FIGS. 7D-7F ).
  • the vacutainer permits a partial or full fill.
  • the inlet module has two hard plastic parts, that get ultrasonically welded together and foil sealed to form a network of channels to allow a flow path to form into the first well overflow to the second sample well.
  • a soft vacutainer seal part is used to for a seal with the vacutainer, and includes a port for sample flow, and a venting port. To overcome the flow resistance once the vacutainer is loaded and inverted, some hydrostatic pressure is needed. Every time sample is removed from a sample well, the well will get replenished by flow from the vacutainer.
  • a modular cartridge can provide a simple means for cross contamination control during certain assays, including but not limited to distribution of PCR products into multiple detection aliquots.
  • a modular cartridge can be compatible with automated fluid dispensing, and provides a way to hold reagents at very small volumes for long periods of time (in excess of a year).
  • pre-dispensing these reagents allows concentration and volumetric accuracy to be set by the manufacturing process and provides for a point of care use instrument that is more convenient as it can require much less precise pipetting.
  • the modular cartridge of the invention is a cartridge that is separated into modules that can be packaged and if necessary sterilized separately. They can also be handled and stored separately, if for example the reagent module requires refrigeration but the detection module does not.
  • FIG. 6 shows a representative cartridge with an inlet module, a reagent module and a detection module that are snapped together.
  • the inlet module would be packaged separately in a sterile package and the reagent and detection modules would be pre-assembled and packaged together.
  • the reagent module could be stored in a refrigerator while the inlet module could be stored in dry storage. This provides the additional advantage that only a very small amount of refrigerator or freezer space is required to store many assays.
  • the operator would retrieve a detection module and open the package, potentially using sterile technique to prevent contamination with skin flora if required by the assay.
  • the Vacutainer tube is then decapped and the inverted inlet module is placed onto the tube as shown in FIG. 7A .
  • This module has been designed to be easily moldable using single draw tooling as shown in FIGS. 7B and 7C and the top and bottom of the cartridge are sealed with foil to prevent contamination and also to close the channels.
  • the inlet section includes a well with an overflow that allows sample tubes with between 2 and 6 ml of blood to be used and still provide a constant depth interface to the system automation. It accomplishes this by means of the overflow shown in FIG. 8 , where blood that overflows the sampling well simply falls into the cartridge body, preventing contamination.
  • FIGS. 9A-9C show the means of storing precisely pipetted small volume reagents.
  • the reagents are kept in pipette tips that are shown in FIG. 9C .
  • These are filled by manufacturing automation and then are placed into the cartridge to seal their tips in tight fitting wells which are shown in a cutaway view FIG. 9B .
  • foil seals are placed on the back of the tips to provide a complete water vapor proof seal. It is also possible to seal the whole module with a seal that will be removed by the operator, either in place of or in addition to the aforementioned foils.
  • This module also provides storage for empty reaction vessels and pipette tips for use by the instrument while the detection module provides storage for capped 200 ⁇ l PCR vials used by the instrument to make final measurements from.
  • FIGS. 10-13C show an alternative embodiment of the detection module of the cartridge which is design to provide for contamination control during, for example, pipetting of post-PCR (polymerase chain reaction) products. This is required because the billion fold amplification produced by PCR presents a great risk of cross contamination and false positives. However, it is desirable to be able to aliquot this mixture safely, because low frequency analytes will have been amplified up and can be distributed for separate detection or identification. There are three ways in which this portion of the cartridge aids in contamination control during this aliquoting operation.
  • the cartridge contains a recessed well to perform the transfer operations in as shown in FIGS. 10A and 10B .
  • the machine provides airflow through this well and down into the cartridge through holes in the bottom of the well, as shown in FIG. 11 .
  • the depth of the well is such that a pipette tip will remain in the airflow and prevent any aerosol from escaping.
  • FIG. 12 depicts a bottom view of the detection module, showing the bottom of the detection tubes and the two holes used to ensure airflow.
  • An optional filter can be inserted here to capture any liquid aerosol and prevent it from entering the machine. This filter could also be a sheet of a hydrophobic material like Gore-tex that will allow air but not liquids to escape.
  • each 200 ul tube there is a special seal cap on each 200 ul tube to provide a make then break seal for each pipette tip as it enters the vessel, as shown in FIGS. 13A-13C . It is contemplated that the pipette tip used for aliqouting be stored in this well at all, thus making it possible for the tip never to leave the controlled air flow region.
  • the modular cartridge is designed for a multiplexed assay.
  • the challenge in multiplexing assays is combining multiple assays which have incompatible assay requirements (i.e., different incubation times and/or temperatures) on one cartridge.
  • the cartridge format depicted in FIGS. 14A-14C allows for the combination of different assays with dramatically different assay requirements.
  • the cartridge features two main components: (i) a reagent module (i.e., the reagent strip portion) that contains all of the individual reagents required for the full assay panel, and (ii) the detection module.
  • the detection modules contain only the parts of the cartridge that carry through the incubation, and can carry single assays or several assays, as needed.
  • the detection module depicted in FIG. 14B includes two detection chambers for a single assay, the first detection chamber as the control and the second detection chamber for the sample. This cartridge format is expandable in that additional assays can be added by including reagents and an additional detection module.
  • the operation of the module begins when the user inserts the entire or a portion of the cartridge into the instrument.
  • the instruments performs the assay actuation, aliquoting the assays into the separate detection chambers. These individual detection chambers are then disconnected from the reagent strip and from each other, and progress through the system separately. Because the reagent module is separated and discarded, the smallest possible sample unit travels through the instrument, conserving internal instrument space. By splitting up each assay into its own unit, different incubation times and temperatures are possible as each multiplexed assay is physically removed from the others and each sample is individually manipulated.
  • the cartridge units of the invention can include one or more populations of magnetic particles, either as a liquid suspension or dried magnetic particles which are reconstituted prior to use.
  • the cartridge units of the invention can include a compartment including from 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles (e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , 1 ⁇ 10 10 to 1 ⁇ 10 12 , 1 ⁇ 10 11 to 1 ⁇ 13, or from 1 ⁇ 10 7 to 5 ⁇ 10 8 magnetic particles) for assaying a single liquid sample.
  • 1 ⁇ 10 6 to 1 ⁇ 10 13 magnetic particles e.g., from 1 ⁇ 10 6 to 1 ⁇ 10 8 , 1 ⁇ 10 7 to 1 ⁇ 10 9 , 1 ⁇ 10 8 to 1 ⁇ 10 10 , 1 ⁇ 10 9 to 1 ⁇ 10 11 , 1 ⁇ 10 10 to 1 ⁇ 10 12 , 1 ⁇ 10 11 to 1 ⁇ 13, or from 1 ⁇ 10 7 to 5 ⁇ 10 8 magnetic particles
  • the systems for carrying out the methods of the invention can include one or more magnetic assisted agglomeration (MAA) units to expedite agglomeration of the magnetic particles, allowing the assay reactions to reach completion (i.e., a stable reading) more quickly.
  • the methods of the invention utilize functionalized magnetic particles to interact with analytes or multivalent binding agents (with multiple binding sites). Agglomeration of the magnetic particles alters the spin-spin relaxation rate of the sample when exposed to a magnetic field with a subsequent change in T 2 relaxation time.
  • a field gradient can be used to sweep magnetic particles (MPs) through the liquid sample, allowing the magnetic particles to bind to either specific antibody (analyte-coated magnetic particles) or analyte (antibody-coated magnetic particles), and then concentrating the magnetic particles in a portion of the reaction chamber so as to facilitate particle-particle interactions that lead to specific, ligand/analyte induced agglomeration.
  • the magnetic particles can optionally be allowed to diffuse in the absence of a magnetic field, sonicated, vortexed, shaken, or subjected to ultrasonic mixing to break apart non-specific magnetic particle interactions and re-distribute the magnetic particles back into the liquid sample. The process can be repeated to promote further specific agglomeration.
  • This cycling of magnetic particles between being dispersed in the liquid sample and then concentrated at the side or bottom of the reaction vessel can be repeated as many times as necessary to maximize specific agglomeration, and consequently maximize the assay signal.
  • the agglomeration state of the magnetic particles can be determined using an NMR relaxation measurement.
  • the MAA method of the invention can employ a gradient magnetic field in order to promote rapid magnetic particle-particle interactions.
  • analyte coated magnetic particles are added to a solution with a multimeric-analyte specific ligand and placed in a gradient magnetic field.
  • the magnetic field causes particles to concentrate on the side or bottom of a reaction vessel (highest magnetic field strength) resulting in enhanced particle-particle interaction and subsequent aggregation. Aggregation is measured by observing a change in, for example, T 2 signal. Improvements of 10 to 1000 percent signal change (e.g., from 10 to 30%, from 20% to 50%, from 40% to 80%, from 50% to 200%, from 100% to 500%, or from 500% to 1000% signal change) can be observed.
  • the cycling MAA approach described herein can accelerate the kinetics of magnetic particle-analyte clustering by (i) reducing the spatial entropy of the binding interaction step by maintaining local concentration of the magnetic particles, (ii) introducing localized mixing by magnet mediated transportation of the pellet from position to position, (iii) reducing shearing of the specific-bound clusters by reducing the need for more energetic dispersion methods, such as vortexing, and/or (iv) changing the magnetic field direction, and thereby causing a local dispersion and re-aggregation of magnetically clustered particles as they re-align their dipoles with the new magnetic field direction, and allowing the locally dispersed magnetic particles to form specific binding interactions involving the target analyte.
  • magnet assemblies producing a magnetic field gradient are placed in two positions relative to the assay tube, one to the side of the tube and one at the bottom of the tube (side-bottom configuration).
  • the second magnet position can be located on a different side of the tube (side-side configuration). The tube then is moved to ensure exposure to one magnet followed by exposure to the other magnet (see FIG. 15 ). This has also been observed to produce a similar enhancement in clustering.
  • An alternate methodology is to rotate the liquid sample within a gradient magnetic field (or to rotate the magnetic field gradient about the sample) to simultaneously effect a re-orientation of particles within the pellet (relative to the remainder of the liquid sample) and to sweep the pellet through the liquid sample.
  • the rate of rotation can be slow to allow the pellet of magnetic particles to largely remain held in proximity to the gradient magnet (rather than moving in concert with the solvent and analytes in liquid sample).
  • the rotation is typically slower than 0.0333 Hz (e.g., from 0.000833 Hz to 0.0333 Hz, from 0.00166 Hz to 0.0333 Hz, or from 0.00333 Hz to 0.0333 Hz), such that the particles are retained adjacent to the magnetic field source, while the remaining contents in the tube are rotated.
  • 0.0333 Hz e.g., from 0.000833 Hz to 0.0333 Hz, from 0.00166 Hz to 0.0333 Hz, or from 0.00333 Hz to 0.0333 Hz
  • a single gradient magnet can be used, while the sample can be moved around the magnet (or use the same location close to the magnet and alternate with a position removed from the field of the single magnet.
  • the magnet could be moved to the proximity or away from the sample.
  • the sample can be placed between magnets of the same field orientation for a “field averaging” effect in alternating fashion, in order to simplify the fabrication of a gMAA system (i.e., eliminate the need to carefully select magnets that generate same field profiles).
  • a plurality of such magnets could be placed in a circular setup, and samples rotated via a carousel setup, from the first magnet to a null (small magnetic field exposure) to the second magnet etc.
  • the rotary gMAA device can include a fixed baseplate to which an electric motor is attached, with a number of magnets mounted around it in a circular pattern. The magnets are spaced such that there is minimal magnetic interference between positions.
  • a carousel capable of holding sample vials is attached to the motor shaft such that it rotates with the motor, exposing the samples to different magnetic field orientations from one position to the next. Any combination of side-oriented magnets, bottom-oriented magnets and positions with very low residual field (null) can be used. See FIG. 56A .
  • a homogenous field is used to expedite the agglomeration of magnetic particles in an assay of the invention.
  • hMAA is not as effective as exposure to field gradients in terms of concentrating particles and sweeping them through the sample, for timescales relevant to applications.
  • hMAA has advantages over the field gradient assisted agglomeration method. Using hMAA the magnetic particles are not enticed to move towards a specific location in the tube (see FIG. 16 ), minimizing non-specific trapping of particles within specific cluster fragments. Agitation after hMAA appears to minimize the non-specific binding.
  • the hMAA treatment appears to enhance analyte induced clustering by increasing the collision frequency (a possible result of decreasing the particle's position and rotational entropies due to localization in an ordered state).
  • the magnetic particles can subsequently be sonicated, vortexed, shaken (i.e., energy additions) to break apart any non-specific particle interactions and re-distribute the particles back into the sample. Additional mixing or gentle agitation during this process would potentially further increase the analyte-specific binding events for enhancement of the overall assay signal.
  • the agglomeration/clustering state of the magnetic particles can be determined by monitoring changes in an NMR relaxation rate. It is also possible to rotate the liquid sample within a homogenous magnetic field (or to rotate a homogenous magnetic field about the sample) to expedite the aggregation of magnetic particles in a liquid sample.
  • the systems of the invention can include one or more MAA units.
  • the MAA unit can be one or more magnets configured to apply a gradient magnetic field in a first direction relative to the liquid sample, and, after repositioning the sample chamber, apply a gradient magnetic field in a second direction relative to the liquid sample (see FIG. 17 ).
  • the MAA unit can be an array of magnets configured to apply a gradient magnetic field to, e.g., the side of a liquid sample, and, after repositioning the sample chamber, to, e.g., the bottom of the liquid sample (see FIGS. 18A-18C ).
  • the systems of the invention can include an MAA unit configured to apply a homogenous magnetic field to one or more liquid samples (see FIGS. 19A and 19B ).
  • the systems for carrying out the methods of the invention can include one or more agitation units to break apart non-specific magnetic particle interactions and re-distribute the magnetic particles back into the liquid sample, or to simply agitate the sample tube to completely mix the assay reagents.
  • the agitation units can include a sonication, vortexing, shaking, or ultrasound station for mixing one or more liquid samples. Mixing could be achieved by aspiration dispensing or other fluid motion (e.g., flow within a channel). Also, mixing could be provided by a vibrating pipette or a pipette that moves from side to side within the sample tube.
  • the agitation unit can be vortexer or a compact vortexer each of which can be designed to provide a stable motion for the desired sample mixing.
  • the vortexer includes the following components: (i) a sample support, (ii) a main plate, (iii) four linkages, (iv) linear rail and carriage system ( ⁇ 2), (v) a support for driveshaft and rails, (vi) coupling and driveshaft, (vii) a mounting plate, and (viii) a drive motor (see FIG. 20 ).
  • the compact vortexer includes the following components: (i) a sample support, (ii) a main plate, (iii) two linkages, (iv) linear rail and carriage system ( ⁇ 1), (v) a support for linear rail, (vi) support for driveshaft, (vii) coupling and driveshaft, (viii) a mounting plate, and (ix) a drive motor (see FIG. 21 ).
  • the basic principle of motion for a vortexer is as follows: the driveshaft including one axis coaxial to the motor shaft, and a second that is offset and parallel to the motor shaft.
  • the offset axis of the driveshaft is driven in an orbital path.
  • the typical offset is 1 ⁇ 4′′ to produce a vortex in a single 0.2 mL sample tube, but this can be easily modified to effectively mix different sample volumes in other tube geometries.
  • the vortexer can be of the type utilizing a planetary belt drive (see FIGS. 23A-23C ).
  • FIG. 23A is an overall view showing the vortexer configured for 1 large tube.
  • FIG. 23B is a section view showing 2 tube holders for small tubes.
  • FIG. 23C is an overall view of vortexer showing 4 tubes and a close-up of planetary belt drive mechanism.
  • the drive motor is typically a servo or stepper with an encoder. These motors have an “index” mark that allows the motor to find a specific point in its rotation. These index marks are used to home the system, and ensure that the sample can be returned to a known position after mixing. Knowing the exact position of the sample in the vortex station allows theses vortexers to be easily accessed by robotic actuators and thus integrated into an automated system.
  • sensing devices external could be employed (see FIG. 22A ). These could be mechanical, magnetic, optical or other sensor that is capable of resolving the sample's position at any point along the system's path or at a fixed “home” position.
  • the system can include using an index mark or external switch to “home” the system to a set position after running, using a sensor which tracks the sample motion at all times, so that wherever the system stops the robot knows the position, and using a “find” method that includes finding a sample after running that would employ a vision system that tracks the sample.
  • the guide mechanism is depicted in FIG. 22B .
  • the main plate is connected to the offset axis of the drive shaft and is free to rotate. The plate follows the orbital path around and dictated by the motor shaft. One end of a linkage is connected to the main plate, and is free to rotate.
  • the two vortexers differ because of their use and design requirements.
  • the compact version is designed to occupy less space, and requires less durability than this version because it is run at a lower speed, as limited by its smaller motor. For these reasons only two linkages are used to connect to a single linear rail system in the compact vortexer. This version needs to be capable of higher speeds, and a nearly continuous utilization due to the large throughput capability of this system. For these reasons a second carriage and set of linkages is added to balance the system, and increase its durability.
  • the systems for carrying out the methods of the invention can include one or more NMR units, MAA units, cartridge units, and agitation units. Such systems may further include other components for carrying out an automated assay of the invention, such as a PCR unit for the detection of oligonucleotides; a centrifuge, a robotic arm for delivery an liquid sample from unit to unit within the system; one or more incubation units; a fluid transfer unit (i.e., pipetting device) for combining assay reagents and a biological sample to form the liquid sample; a computer with a programmable processor for storing data, processing data, and for controlling the activation and deactivation of the various units according to a one or more preset protocols; and a cartridge insertion system for delivering pre-filled cartridges to the system, optionally with instructions to the computer identifying the reagents and protocol to be used in conjunction with the cartridge. See FIG. 42 .
  • the systems of the invention can provide an effective means for high throughput and real-time detection of analytes present in a bodily fluid from a subject.
  • the detection methods may be used in a wide variety of circumstances including, without limitation, identification and/or quantification of analytes that are associated with specific biological processes, physiological conditions, disorders or stages of disorders.
  • the systems have a broad spectrum of utility in, for example, drug screening, disease diagnosis, phylogenetic classification, parental and forensic identification, disease onset and recurrence, individual response to treatment versus population bases, and monitoring of therapy.
  • the subject devices and systems are also particularly useful for advancing preclinical and clinical stage of development of therapeutics, improving patient compliance, monitoring ADRs associated with a prescribed drug, developing individualized medicine, outsourcing blood testing from the central laboratory to the home or on a prescription basis, and monitoring therapeutic agents following regulatory approval.
  • the devices and systems can provide a flexible system for personalized medicine.
  • the system of the invention can be changed or interchanged along with a protocol or instructions to a programmable processor of the system to perform a wide variety of assays as described herein.
  • the systems of the invention offer many advantages of a laboratory setting contained in a desk-top or smaller size automated instrument.
  • the systems of the invention can be used to simultaneously assay analytes that are present in the same liquid sample over a wide concentration range, and can be used to monitor the rate of change of an analyte concentration and/or or concentration of PD or PK markers over a period of time in a single subject, or used for performing trend analysis on the concentration, or markers of PD, or PK, whether they are concentrations of drugs or their metabolites.
  • concentration of glucose in a sample at a given time as well as the rate of change of the glucose concentration over a given period of time could be highly useful in predicting and avoiding, for example, hypoglycemic events.
  • the data generated with the use of the subject fluidic devices and systems can be utilized for performing a trend analysis on the concentration of an analyte in a subject.
  • a patient may be provided with a plurality of cartridge units to be used for detecting a variety of analytes at predetermined times.
  • a subject may, for example, use different cartridge units on different days of the week.
  • the software on the system is designed to recognize an identifier on the cartridge instructing the system computer to run a particular protocol for running the assay and/or processing the data.
  • the protocols on the system can be updated through an external interface, such as an USB drive or an Ethernet connection, or in some embodiments the entire protocol can be recorded in the barcode attached to the cartridge.
  • the protocol can be optimized as needed by prompting the user for various inputs (i.e., for changing the dilution of the sample, the amount of reagent provided to the liquid sample, altering an incubation time or MAA time, or altering the NMR relaxation collection parameters).
  • a multiplexed assay can be performed using a variety of system designs.
  • a multiplexed assay can be performed using any of the following configurations: (i) a spatially-based detection array can be used to direct magnetic particles to a particular region of a tube (i.e., without aggregation) and immobilize the particles in different locations according to the particular analyte being detected.
  • the immobilized particles are detected by monitoring their local effect on the relaxation effect at the site of immobilization.
  • the particles can be spatially separated by gravimetric separation in flow (i.e., larger particles settling faster along with a slow flow perpendicular to gravity to provide spatial separation based on particle size with different magnetic particle size populations being labeled with different targets).
  • capture probes can be used to locate magnetic particles in a particular region of a tube (i.e., without aggregation) and immobilize the particles in different locations (i.e., on a functionalized surface, foam, or gel).
  • the array is flow through system with multiple coils and magnets, each coil being a separate detector that has the appropriate particles immobilized within it, and the presence of the analyte detected with signal changes arising from clustering in the presence of the analyte.
  • each individual analyte in the multiplexed assay can be detected by sliding a coil across the sample to read out the now spatially separated particles.
  • a microfluidic tube where the sample is physically split amongst many branches and a separate signal is detected in each branch, each branch configured for detection of a separate analyte in the multiplexed assay.
  • An array of 96 wells (or less or more) where each well has its own coil and magnet, and each well is configured for detection of a separate analyte in the multiplexed assay.
  • a sipper or flow through device with multiple independently addressable coils inside one magnet or inside multiple mini magnets that can be used for sequential readings, each reading being a separate reaction for detection of a separate analyte in the multiplexed assay.
  • a tube containing two compartments read simultaneously, resulting in one relaxation curve which is then fit using bi-exponential fitting to produce the separate readings for the multiplexed array.
  • Sequential measurements using magnetic separation and resuspension requires novel binding probes or the ability to turn them on and off.
  • the gel or viscous solution enhances spatial separation of more than one analyte in the starting sample because after the sample is allowed to interact with the gel, the target analyte can readily diffuse through the gel and specifically bind to a conjugated moiety on the gel or viscous solution held nanoparticle.
  • the clustering or aggregation of the specific analyte, optionally enhanced via one of the described magnetic assisted agglomeration methods, and detection of analyte specific clusters can be performed by using a specific location NMR reader. In this way a spatial array of nanoparticles, and can be designed, for example, as a 2d array. (xi) Magnetic particles can be spotted and dried into multiple locations in a tube and then each location measured separately.
  • one type of particle can be bound to a surface and a second particle suspended in solution, both of which hybridize to the analyte to be detected.
  • Clusters can be formed at the surface where hybridization reactions occur, each surface being separately detectable.
  • a spotted array of nucleic acids can be created within a sample tube, each configured to hybridize to a first portion of an array of target nucleic acids.
  • Magnetic particles can be designed with probes to hybridize to a second portion of the target nucleic acid. Each location can be measured separately.
  • any generic beacon or detection method could be used to produce output from the nucleic acid array.
  • An array of magnetic particles for detecting an array of targets can be included in a single sample, each configured (e.g., by size, or relaxation properties) to provide a distinct NMR relaxation signature with aggregate formation.
  • each of the particles can be selected to produce distinct T2 relaxation times (e.g., one set of particles covers 10-200 ms, a second set from 250-500 a third set from 550-1100, and so on). Each can be measured as a separate band of relaxation rates.
  • a single sample with multiple analytes and magnetic particles can undergo separation in the presence of a magnetic or electric field (i.e., electrophoretic separation of magnetic particles coated with analytes), the separate magnetic particles and/or aggregates reaching the site of a detector at different times, accordingly.
  • the detection tube could be separated into two (or more) chambers that each contain a different nanoparticle for detection.
  • the tube could be read using the reader and through fitting a multiple exponential curve such as A*exp(T2_1)+B*exp(T2_2), the response of each analyte could be determined by looking at the relative size of the constants A and B and T2_1 and T2_2.
  • Gradient magnetic fields can be shimmed to form narrow fields. Shim pulses or other RF based Shimming within a specific field can be performed to pulse and receive signals within a specific region. In this way one could envision a stratification of the Rf pulse within a shim and specific resonance signals could be received from the specific shim.
  • Nanoparticles having two distinct NMR relaxation signals upon clustering with an analyte may be employed in a multiplexed assay. In this methods, the observation that small particles (30-200 nm) cause a decrease in T2 with clustering whereas large particles (>800 nm) cause an increase with clustering.
  • the reaction assay is designed as a competitive reaction, so that with the addition of the target it changes the equilibrium relaxation signal. For example, if the T2 relaxation time is shorter, clusters forming of analyte with small particles are forming. If on the other hand, the T2 relaxation becomes longer, clusters of analyte with larger particles are forming. It's probably useful to change the density/viscosity of the solution with additives such as trehalose or glucose or glycerol to make sure the big particles stay in solution.
  • additives such as trehalose or glucose or glycerol
  • One nanoparticle having binding moieties to a specific analyte for whose T2 signal is decreased on clustering may be combined with a second nanoparticle having a second binding moiety to a second analyte for whose T2 signal is increased on clustering.
  • the sample is suspected to have both analytes and the clustering reaction may cancel each other out (the increased clustering cancels the decreased clustering)
  • an ordering of the analysis i.e. addition of competitive binding agents to detect a competitive binding and thus T2 signal that would be related to the presence/absence of the analyte of interest in the sample.
  • the magnetic nanoparticle conjugated with probe anneals to one specific sequence on the target analyte and the other particle binds to another sequence on the target nucleic acid sequence.
  • These clusters will be big enough to precipitate (this step may require a centrifugation step).
  • One possible different detection technique includes phase separated signals, which would stem from differing RF coil pulse sequences that are optimized for the conjugated nanoparticle-analyte interaction.
  • multiple coils in an array that would optimize the ability of the different RF pulses and relaxation signal detection to be mapped and differentiated to ascertain the presence/absence of more than one analyte.
  • Multiplexing may also employ the unique characteristic of the nanoparticle-analyte clustering reaction and subsequent detection of water solvent in the sample, the ability of the clusters to form various “pockets” and these coordinated clusters to have varying porosity.
  • linkers having varying length or conformational structures can be employed to conjugate the binding moiety to the magnetic nanoparticle.
  • the methods of the invention can include a fluorinated oil/aqueous mixture for capturing particles in an emulsion.
  • the hydrophic capture particle set is designed to bind and aggregate more readily in an hydrophobic environment
  • the aqueous capture particle set is designed to bind and aggregate in an aqueous environment.
  • the detection tube may have a capsular design to enhance the ability to move the capsules through an MR detector to read out the signal.
  • additional use of a fluorescent tag to read out probe identity may be employed, i.e. in the case of two different analytes in the same aqueous or hydrophic phase, the addition of a fluorescent tag can assist determination of the identify of the analyte.
  • oligonucleotide capture probes that are conjugated to the magnetic nanoparticles are designed so that specific restriction endonuclease sites are located within the annealed section. After hybridization with the sample forming nanoparticle-analyte clusters, a relaxation measurement then provides a base signal.
  • a magnetic nanoparticle is conjugated with two separate and distinct binding moieties, i.e. an oligonucleotide and an antibody. This nanoparticle when incubated with a sample having both types of analytes in the sample will form nanoparticle-analyte complexes, and a baseline T2 relaxation signal will be detectable.
  • Subsequent addition of a known concentration of one of the analytes can be added to reduce the clustering formed by that specific analyte from the sample.
  • a subsequent T2 relaxation signal is detected and the presence/absence of the sample analyte can be surmised.
  • a second analyte can be added to compete with the analyte in the sample to form clusters. Again, after a subsequent T2 relaxation signal detection the presence/absence of the second sample analyte can be surmised. This can be repeated.
  • a multiplexed assay employing the methods of this invention can be designed so that the use of one non-superparamagnetic nanoparticle to generate clusters with analyte from a sample, will reduce the overall Fe2+ in assay detection vessel and will extend the dynamic range so that multiple reactions can be measured in the same detection vessel.
  • Multiplexing nucleic acid detection can make use of differing hybridization qualities of the conjugated magnetic nanoparticle and the target nucleic acid analyte.
  • capture probes conjugated to magnetic nanoparticles can be designed so that annealing the magnetic nanoparticle to the target nucleic acid sequence is different for more than one nucleic acid target sequence.
  • Factors for the design of these different probe-target sequences include G-C content (time to form hybrids), varying salt concentration, hybridization temperatures, and/or combinations of these factors.
  • This method then would entail allowing various nucleic acid conjugated magnetic nanoparticles to interact with a sample suspected of having more than one target nucleic acid analyte. Relaxation times detected after various treatments, i.e. heating, addition of salt, hybridization timing, would allow for the ability to surmise which suspected nucleic acid sequence is present or absent in the sample.
  • oligonucleotide conjugated to magnetic nanoparticles are added to the sample and a relaxation measurement is taken. The sample is then exposed to a temperature to melt the oligonucleotide-analyte interaction and addition of a oligonucleotide that is not attached to a magnetic nanoparticle is added to compete away any analyte binding to the magnetic nanoparticle.
  • a second magnetic nanoparticle having a second oligonucleotide conjugated to it is then added to form clusters with a second specific target nucleic acid analyte.
  • the method could have a step prior to the addition of the second magnetic nanoparticle that would effectively sequester the first magnetic nanoparticle from the reaction vessel, i.e. exposing the reaction vessel to a magnetic field to move the particles to an area that would not be available to the second, or subsequent reaction.
  • Each of the multiplexing methods above can employ a step of freezing the sample to slow diffusion and clustering time and thus alter the measurement of the relaxation time. Slowing the diffusion and clustering of the method may enhance the ability to separate and detect more than one relaxation time.
  • Each of the multiplexing methods above can make use of sequential addition of conjugated nanoparticles followed by relaxation detection after each addition. After each sequential addition, the subsequent relaxation baseline becomes the new baseline from the last addition and can be used to assist in correlating the relaxation time with presence/absence of the analyte or analyte concentration in the sample.
  • Hidden capture probes In this method of multiplexing, oligonucleotides conjugated to the magnetic nanoparticles are designed so that secondary structure or a complementary probe on the surface of the particle hides or covers the sequence for hybridization initially in the reaction vessel. These hidden hybridization sequences are then exposed or revealed in the sample vessel spatially or temporally during the assay. For example, as mentioned above, hybridization can be affected by salt, temperature and time to hybridize.
  • secondary or complementary structures on the oligonucleotide probe conjugated to the magnetic nanoparticle can be reduced or relaxed to then expose or reveal the sequence to hybridize to the target nucleic acid sample. Further, secondary structures could be reduced or relaxed using a chemical compound, e.g. DMSO.
  • Another method to selectively reveal or expose a sequence for hybridization of the oligonucleotide conjugated nanoparticle with the target analyte is to design stem-loop structures having a site for a restriction endonuclease; subsequent digestion with a restriction endonuclease would relax the stem-loop structure and allow for hybridization to occur.
  • a chemical cut of the stem-loop structure, releasing one end could make the sequence free to then hybridize to the target nucleic acid sequence.
  • the assay can include a multiplexed PCR to generate different amplicons and then serially detect the different reactions.
  • the multiplexed assay optionally includes a logical array in which the targets are set up by binary search to reduce the number of assays required (e.g., gram positive or negative leads to different species based tests that only would be conducted for one group or the other).
  • the systems of the invention can run a variety of assays, regardless of the analyte being detected from a bodily fluid sample.
  • a protocol dependent on the identity of the cartridge unit being used can be stored on the system computer.
  • the cartridge unit has an identifier (ID) that is detected or read by the system computer, or a bar code (1D or 2D) on a card that then supplies assay specific or patient or subject specific information needed to be tracked or accessed with the analysis information (e.g., calibration curves, protocols, previous analyte concentrations or levels).
  • ID identifier
  • the cartridge unit identifier is used to select a protocol stored on the system computer, or to identify the location of various assay reagents in the cartridge unit.
  • the protocol to be run on the system may include instructions to the controller of the system to perform the protocol, including but not limited to a particular assay to be run and a detection method to be performed.
  • the identifier may be a bar code identifier with a series of black and white lines, which can be read by a bar code reader (or another type of detector) upon insertion of the cartridge unit.
  • Other identifiers could be used, such as a series of alphanumerical values, colors, raised bumps, RFID, or any other identifier which can be located on a cartridge unit and be detected or read by the system computer.
  • the detector may also be an LED that emits light which can interact with an identifier which reflects light and is measured by the system computer to determine the identity of a particular cartridge unit.
  • the system includes a storage or memory device with the cartridge unit or the detector for transmitting information to the system computer.
  • the systems of the invention can include an operating program to carry out different assays, and cartridges encoded to: (i) report to the operating program which pre-programmed assay was being employed; (ii) report to the operating program the configuration of the cartridges; (iii) inform the operating system the order of steps for carrying out the assay; (iv) inform the system which pre-programmed routine to employ; (v) prompt input from the user with respect to certain assay variables; (vi) record a patient identification number (the patient identification number can also be included on the Vacutainer holding the blood sample); (vii) record certain cartridge information (i.e., lot #, calibration data, assays on the cartridge, analytic data range, expiration date, storage requirements, acceptable sample specifics); or (viii) report to the operating program assay upgrades or revisions (i.e., so that newer versions of the assay would occur on cartridge upgrades only and not to the larger, more costly system).
  • the operating program assay upgrades or revisions i.e., so that new
  • the systems of the invention can include one or more fluid transfer units configured to adhere to a robotic arm (see FIGS. 43A-43C ).
  • the fluid transfer unit can be a pipette, such as an air-displacement, liquid backed, or syringe pipette.
  • a fluid transfer unit can further include a motor in communication with a programmable processor of the system computer and the motor can move the plurality of heads based on a protocol from the programmable processor.
  • the programmable processor of a system can include instructions or commands and can operate a fluid transfer unit according to the instructions to transfer liquid samples by either withdrawing (for drawing liquid in) or extending (for expelling liquid) a piston into a closed air space.
  • Both the volume of air moved and the speed of movement can be precisely controlled, for example, by the programmable processor.
  • Mixing of samples (or reagents) with diluents (or other reagents) can be achieved by aspirating components to be mixed into a common tube and then repeatedly aspirating a significant fraction of the combined liquid volume up and down into a tip. Dissolution of reagents dried into a tube can be done is similar fashion.
  • a system can include one or more incubation units for heating the liquid sample and/or for control of the assay temperature. Heat can be used in the incubation step of an assay reaction to promote the reaction and shorten the duration necessary for the incubation step.
  • a system can include a heating block configured to receive a liquid sample for a predetermined time at a predetermined temperature. The heating block can be configured to receive a plurality of samples.
  • the system temperature can be carefully regulated.
  • the system includes a casing kept at a predetermined temperature (i.e., 37° C.) using stirred temperature controlled air. Waste heat from each of the units will exceed what can be passively dissipated by simple enclosure by conduction and convection to air.
  • the system can include two compartments separated by an insulated floor. The upper compartment includes those portions of the components needed for the manipulation and measurement of the liquid samples, while the lower compartment includes the heat generating elements of the individual units (e.g., the motor for the centrifuge, the motors for the agitation units, the electronics for each of the separate units, and the heating blocks for the incubation units). The lower floor is then vented and forced air cooling is used to carry heat away from the system. See FIGS. 44A and 44B .
  • the MR unit may require more closely controlled temperature (e.g., ⁇ 0.1° C.), and so may optionally include a separate casing into which air heated at a predetermined temperature is blown.
  • the casing can include an opening through which the liquid sample is inserted and removed, and out of which the heated air is allowed to escape. See FIGS. 45A and 45B .
  • Other temperature control approaches may also be utilized.
  • Particles were washed away from free dextran 3 ⁇ in 1 ml of PBS using magnetic separation, then resuspended in 1 ml of PBS.
  • 100 ⁇ l of a 100 mM solution of Sulfo-NHS-biotin (Invitrogen) was used to decorate the amino groups on the dextran surface with biotin.
  • particles were washed 3 ⁇ in 1 ml activation buffer.
  • a protein block of 100 ⁇ l of 0.5 mg/ml of bovine serum albumin (BSA) (Sigma) and 30 ⁇ l of 10 mg/ml EDC was introduced and incubated overnight (Sigma). Prepared particles were washed 3 ⁇ in 1 ml PBS and resuspended to the desired concentration.
  • BSA bovine serum albumin
  • biotin decorated amino-dextran magnetic particles prepared according to the method described in Example 1 were assayed in PBS and in 20% lysed blood samples in an anti-biotin titration T 2 assay.
  • the assay was performed with the following procedure. 50 ⁇ L of matrix, either PBS or 20% Lysed blood sample, 50 ⁇ L of varying concentrations of Anti-biotin antibody, and 50 ⁇ L of 1.0 ⁇ g/ml secondary antibody were added to a 5 mm NMR Tube. 150 ⁇ L of 0.02 mM Fe particles were then added to each tube (i.e., 2.7 ⁇ 10 8 particles per tube). The samples were then vortexed for 4 seconds and incubated in a 37° C. heat block for 2 minutes. Each sample was then revortexed for 4 seconds, and incubated for an additional minute in the 37° C. heat block. Following incubation, each sample was placed into a Bruker Minispec for 10 minutes, under a magnetic field.
  • the graph depicted in FIG. 38 compares particles prepared with (open circle) and without (filled circle) a protein blocking step. We have thus found the protein block may be needed to achieve similar functionality in blood matrices.
  • Additional protein blocks including but not limited to fish skin gelatin have also been successful.
  • Particles were prepared according to the method described above, with the exception that in lieu of using BSA as the protein block, fish skin gelatin (FSG) was substituted.
  • FSG fish skin gelatin
  • the graph depicted in FIG. 39 shows results of a T 2 assay (as described above) using antibody titration for particles blocked with BSA and compared to FSG. The data indicates that there is little or no difference between the two protein blocking methods (see FIG. 39 ). However, BSA has proven to be a more reliable block.
  • Bovine Serum Albumin (Sigma Product #: B4287-256)
  • VWR Variable Speed Vortexer
  • Buffer/Analyte Preparation 0.1% BSA, 0.1% Tween® in 1 ⁇ PBS: A 10% Tween® 20 solution by weight was prepared. Briefly, Tween® in 1 ⁇ PBS was prepared. 500 mL of 0.2% Tween solution was prepared by adding 10 mL of 10% Tween® to 490 mL of 1 ⁇ PBS. A 2% solution of BSA was prepared in 1 ⁇ PBS solution by weight. A 0.2% solution of BSA solution was prepared by adding 50 mL of 2% BSA in PBS to 450 mL of 1 ⁇ PBS. Dilutions were combined to make a final volume of 1 L and a final buffer concentration of 0.1% BSA, 0.1% Tween® in 1 ⁇ PBS.
  • PEG-FITC-Biotin Analyte 100 ⁇ l of a 0.5 mM solution was prepared from 1 mM Tris HCl. 40 ⁇ l of PEG FITC biotin was mixed with 40 ⁇ l of 0.5 mM Tris HCl, and incubated for 15 minutes at room temperature. After 15 minutes, 70 ⁇ l of PEG-FITC-Biotin in 0.5 mM Tris HCl was added to 630 ⁇ l of 0.1% Tween® to make a 100 ⁇ M stock solution. Stock solution was vigorously mixed by vortexing. 200 ⁇ l of 100 ⁇ M solution was added to 900 ⁇ l of 0.1% Tween® to make 20,000 nM analyte. 10 fold dilutions were prepared down to 0.02 nM
  • 25 ⁇ l of appropriate analyte and 50 ⁇ l of 1:5 Lysed blood matrix were pipetted directly into a 5 mm NMR tube. Samples were vortexed for 4 seconds. 25 ⁇ l of primary Anti-biotin antibody (0.18 ⁇ g/ml diluted in 0.1% Tween 20, 0.1% BSA, 1 ⁇ PBS) was added, followed by a 37° C. incubation for 15 minutes. After 15 minutes, 50 ⁇ l of 3.0 ⁇ g/ml Secondary Anti-Mouse antibody (diluted in 0.1% Tween, 0.1% BSA, 1 ⁇ PBS) and 150 ⁇ l of 0.02 mM Fe particles (2.7 ⁇ 10 8 particles per tube) were added to the NMR Tube.
  • primary Anti-biotin antibody (0.18 ⁇ g/ml diluted in 0.1% Tween 20, 0.1% BSA, 1 ⁇ PBS) was added, followed by a 37° C. incubation for 15 minutes. After 15 minutes, 50 ⁇ l of 3.0 ⁇ g/ml Secondary
  • the sample was then vortexed for 4 seconds and incubated for 5 minutes at 37° C.
  • the sample was placed in a Bruker Minispec for 10 minutes, under magnetic field. After 10 minutes, the sample was removed from the magnet and incubated for an additional 5 minutes. The sample was again vortexed for 4 seconds and incubated for an additional 1 minute. T 2 values were taken using the Bruker Minispec program with the following parameters:
  • the carboxylated magnetic particles are first conjugated to 10 kDa amino dextran via EDC chemistry as described above.
  • the dextran coated particles are further modified with an excess of sulfo-SMCC to provide a maleimide functional group.
  • Antibodies are modified with a SATA linker, which primarily binds to the amines on the antibody.
  • the SATA linkage is controlled to minimize over-functionalization of the antibody which may lead to cross-linking of the particles or reduced affinity of the antibody.
  • the SATA linker exposes a thiol functional group which can be used to directly attach to the malemide functionalized particles forming a thioether bond.
  • the number of antibodies conjugated to each particle can be measured using a BCA protein assay (Pierce).
  • Linkers that provide similar functionality to SATA have been used successfully, such as SPDP (N-Succinimidyl 3-[2-pyridyldithio]-propionate).
  • Antibody coated magnetic particles can also be prepared using the chemistries described above, but with direct covalent linkage to the base carboxylated particle. In some instances it may necessary to add additional coating to the particle surface, such as dextran, or a blocking agent. Similar chemistries can be used with alternate coatings to the amino dextran, such as PEG or BSA.
  • the assay includes the following: a target sample is incubated in the presence of a magnetic particle that has been decorated with creatinine, which is linked to the surface of the magnetic particles.
  • the creatinine decorated magnetic particles are designed to aggregate in the presence of the creatinine antibody.
  • Each of the creatinine decorated magnetic particles and creatinine antibody is added to the liquid sample containing creatinine, which competes with the magnetic particles for the creatinine antibody.
  • the binding of the creatinine to the antibody blocks agglomeration of the magnetic particles, and low levels of creatinine are marked by the formation of agglomerates.
  • agglomerates alter the spin-spin relaxation rates of sample when exposed to a magnetic field and the change in the T 2 relaxation times (measuring a change in the magnetic resonance signal from the surrounding water molecules) can be directly correlated to presence and/or concentration of the analyte in the target sample.
  • Sulfo-NHS 55 ⁇ mol in 200 ⁇ l MES buffer
  • EDC 33.5 ⁇ mol in 200 ⁇ l MES buffer
  • the solution was
  • COOH-creatinine (66 ⁇ mol), EDC (140 ⁇ mol), and NHS (260 ⁇ mol) were combined with 300 ⁇ l of dry DMSO to form a slurry, which cleared as the reaction reached completion.
  • the creatinine assay protocol was performed using creatinine conjugated particles and soluble creatinine antibody with detection using the T 2 signal was generated/completed.
  • the creatinine competitive assay architecture is depicted in FIG. 24 .
  • Solutions of magnetic particles, antibody, and liquid sample were, where indicated, subject to dilution with an assay buffer that included 100 mM Tris pH 7.0, 800 mM NaCl, 1% BSA, 0.1% Tween®, and 0.05% ProClin®.
  • the creatinine-coated magnetic particles were diluted to 0.4 mM Fe (5.48 ⁇ 10 9 particles/ml) in assay buffer, vortexed thoroughly, and allowed to equilibrate for 24 hours at 4-8° C.
  • the anti-creatinine mouse monoclonal antibody (described above) was employed as a multivalent binding agent for the creatinine-conjugated magnetic particles.
  • the antibody was diluted to a concentration of 0.8 ⁇ g/ml in assay buffer and vortexed thoroughly.
  • Samples and calibrators were diluted 1 part sample to 3 parts assay buffer.
  • the upper assay range is ca. 4 mg/dL creatinine.
  • samples with expected creatinine levels>4 mg/dL an additional sample dilution was performed using 1 part initial diluted sample to 4 parts assay buffer.
  • the pre-diluted sample, assay buffer, magnetic particle, and antibody solutions were each vortexed. 10 ⁇ L of each solution added to a tube, and the tube was vortexed for 5 seconds.
  • the tube was then subjected to 12 minutes of gMAA, incubated for 5 minutes at 37° C., placed in the MR Reader (T 2 MR, Reader with 2200 Fluke Temperature Controller, with NDxlient software 0.9.14.1/hardware Version 0.4.13 Build 2, Firmware Version 0.4.13 Build 0) to measure the T 2 relaxation rate of the sample, and the T 2 relaxation rate of the sample was compared to a standard curve (see FIG. 25A ) to determine the concentration of creatinine in the liquid sample.
  • MR Reader T 2 MR, Reader with 2200 Fluke Temperature Controller, with NDxlient software 0.9.14.1/hardware Version 0.4.13 Build 2, Firmware Version 0.4.13 Build 0
  • the monomeric, biotinylated monomeric, and multimerized forms were then tested with creatinine-coated magnetic particles to assess the effect of increased valency on T 2 time.
  • the results are depicted in FIG. 25C , showing the multimerized antibody forms clusters at much lower concentrations that the non-multimerized antibodies. This valency enhancement for particle clustering has also been observed using IgM antibodies.
  • the assay includes the following: a target sample is incubated in the presence of (i) a magnetic particle that has been decorated with creatinine antibody; and (ii) a multivalent binding agent including multiple creatinine conjugates.
  • the magnetic particles are designed to aggregate in the presence of the multivalent binding agent, but aggregation is inhibited by competition with creatinine in the liquid sample.
  • the binding of the creatinine to the antibody-coated particle blocks agglomeration of the magnetic particles in the presence of the multivalent binding agent, and low levels of creatinine are marked by the formation of agglomerates.
  • agglomerates alter the spin-spin relaxation rates of sample when exposed to a magnetic field and the change in the T 2 relaxation times (measuring a change in the magnetic resonance signal from the surrounding water molecules) can be directly correlated to presence and/or concentration of the analyte in the target sample.
  • the solution was briefly vortexed and placed on an end over end mixer for 1 hour at room temperature.
  • the activated particles were washed with mL PBS-0.01% T20, and resuspended in 1 mL of 10% w/v solution of amine-PEG-amine in PBS-0.01% T20.
  • the mixture was vortexed and placed on an end over end mixer for 2 hours at room temperature, and then washed 3 ⁇ with PBS-0.01% T20.
  • BSA can be substituted for amine-PEG-amine as an alternate chemistry.
  • the BSA-coated magnetic particles were prepared as described in example 6, in the section describing creatinine coated magnetic particles.
  • the particles were resuspended in 260 ⁇ l PBS-0.01% T20 and reacted with 198 ⁇ l sulfo SMCC (5 mg/mL in PBS-0.01% T20).
  • the solution was briefly vortexed and placed on an end over end mixer for 1 hour at room temperature, and then washed 3 ⁇ with PBS-0.01% T20 with 10 mM EDTA to produce SMCC-coated particles.
  • deacetylation buffer 0.5M hydroxylamine hydrochloride in pH 7.4, 10 mM phosphate, 150 mM sodium chloride, 10 mM EDTA
  • SPDP-labeled antibody can be used as an alternate to SATA.
  • SPDP-labeled antibody was prepared by adding SPDP (10 mmol in DMSO) with antibody (2 nmol in PBS, pH 7.4). The solution was incubated for 1 hour at room temperature and purified through a desalting column. The disulfide linkage of SPDP on the SPDP-labeled antibody was cleaved in a reaction with 5 mM mercaptoethyamine and incubated for 10 minutes at ambient temperature. The disulfide bond-cleaved SPDP-labeled antibody was purified through a desalting column prior to use.
  • the SMCC-functionalized particles with PEG- or BSA-coating and deacetylated SATA-modified antibody were combined and placed on an end over end mixer for overnight at room temperature, washed 3 ⁇ with PBS-0.05% Tween® 80, and resuspended in PBS-0.01% T20 with 10 mM EDTA.
  • a blocking agent m-PEG-SH 2K was added, the solution was placed on an end over end mixer for 2 hours, washed 2 ⁇ with PBS-0.05% Tween® 80, and resuspended in PBS-0.05% Tween® 80, 1% BSA, and 0.05% ProClin® to produce antibody-coated magnetic particles.
  • the SMCC-functionalized BSA-coated particles and disulfide-bind cleaved SPDP-labeled antibody were combined and placed on an end over end mixer for 2 hours at room temperature, washed 2 times with PBS-0.01% Tween® 20, 10 mM EDTA, and resuspended in PBS, 0.01% T20, and 10 mM EDTA.
  • a blocking agent, m-PEG-SH 2K (1 mole) was added, and the solution was placed on an end over end mixer for 2 hours.
  • a second blocking agent, n-ethyl maleimide (5 ⁇ mole) was added.
  • the particles were mixed for 15 minutes, washed twice with PBS-0.01% Tween® 20, and resuspended in pH 9, 100 mM Tris, 0.05% Tween® 80, 1% BSA, and 0.05% ProClin® to produce antibody coated magnetic particles.
  • the procedure outlined above can be used with creatinine antibodies, or the creatinine antibodies can be coupled directly to the surface of the carboxylated magnetic particles via EDC coupling.
  • COOH-creatinine was conjugated to 3 amino-dextran compounds (Invitrogen; MW 10 k, 40 k, and 70 k with 6.5, 12, and 24 amino groups per molecule of dextran respectively) and BSA via EDC coupling.
  • the resulting BSA-creatinine and amino-dextran-creatinine multivalent binding agents can be used in the competitive inhibition assay described above. Degrees of substitution between 2-30 creatinines per dextran moiety were achieved. An example creatinine inhibition curve is shown in FIG. 33 .
  • the binding agent used is a 40 kDa dextran with ⁇ 10 creatinines per dextran molecule.
  • Tacrolimus conjugates were prepared using dextran and BSA.
  • FK-506 was subjected to the olefin metathesis reaction using Grubbs second generation catalyst in the presence of 4-vinylbenzoic acid as depicted below in Scheme 1.
  • the crude product mixture was purified by normal phase silica gel chromatography.
  • Dextran-tacrolimus conjugates were prepared using three different molecular weight amino-dextrans, each with a different amino group substitution.
  • Activated Tac solution was added drop-wise with stirring at room temperature to the stock solution of amino-dextran in the ratios tabulated below. Each reaction was stirred vigorously for at least 2 hours.
  • the resulting Tac-dextran conjugates were purified using a 5-step serial dialysis of each reaction product (1 st —15% (v/v) aqueous DMSO; 2 nd —10% (v/v) aqueous methanol; 3 rd to 5 th —high purity water; at least 2 hours for each step; using a 3,500 MWCO dialysis membrane for the 10K MW amino-dextran and a 7K MWCO dialysis membrane for the 40K and 70K amino-dextran).
  • each of the samples was lyophilized and the dry weight determined.
  • the multivalent binding agents were reconstituted prior to use.
  • the tacrolimus substitution ratios were estimated based upon the absorbance at 254 nm.
  • BSA-tacrolimus conjugates were prepared with varying degrees of tacrolimus substitution.
  • 34.5 ⁇ L of NHS solution (66.664 mg/mL in acetonitrile) and 552 ⁇ L of EDC (6.481 mg/mL in 50 mM MES pH 4.7) were combined with stirring.
  • 515.2 ⁇ L of this EDC NHS mixture was added drop-wise to 220.8 ⁇ L. of tacrolimus-acid derivative (C21) solution (33.33 mg/mL in acetonitrile) and the contents stirred for 1 hour at room temperature to form the activated tacrolimus-acid derivative.
  • the activated tacrolimus was used immediately.
  • BSA was dissolved in phosphate buffered saline and acetonitrile to form a solution containing 5 mg/mL BSA in 40% acetonitrile.
  • Activated Tac solution was added drop-wise with stirring at room temperature to the BSA solution in the ratios tabulated below. Each reaction was stirred vigorously for at least 2 hours.
  • the resulting Tac-BSA conjugates were purified using a PD10 size exclusion column pre-equilibrated with 40% acetonitrile. The eluent was collected in 1 mL fractions and monitored for absorbance at 280 nm to identify fractions containing BSA.
  • the BSA-containing fractions were combined and the acetonitrile removed under vacuum.
  • Tac-BSA conjugates were evaluated for clustering ability by performing a titration similar to that used for the dextran-tacrolimus conjugates. As observed, clustering performance differs with Tac substitution ratio (see FIG. 36 ).
  • a tacrolimus assay was developed using anti-tacrolimus antibody conjugated particles and BSA-tacrolimus multivalent binding agent with detection using an MR Reader (see Example 6). This assay was designed for testing whole blood samples that have been extracted to release tacrolimus from the red blood cells and binding proteins (the extraction of hydrophobic analyte from a sample can be achieved, for example, using the methodology described in U.S. Pat. No. 5,135,875).
  • the tacrolimus competitive assay architecture is depicted in FIG. 28 .
  • Solutions of magnetic particles and multivalent binding agent were, where indicated, subject to dilution with an assay buffer that included 100 mM Glycine pH 9, 0.05% Tween® 80, 1% BSA, 150 mM NaCl, 0.1% CHAPS.
  • a base particle with COOH functionality was modified by sequential aminated coating (PEG or BSA), antibody covalent attachment, PEG cap and PEG/protein block (as described in the examples above).
  • the antibody-coated magnetic particles were diluted to 0.4 mM Fe (5.48 ⁇ 10 9 particles/ml) in assay buffer, and vortexed thoroughly.
  • the multivalent binding agent was formed from COOH-modified tacrolimus covalently conjugated to BSA (as described in Example 8).
  • the multivalent binding agent was diluted to 0.02 ⁇ g/ml in assay buffer, and vortexed thoroughly.
  • the extracted sample solution (10 ⁇ L) and the magnetic particle solution (10 ⁇ L) were combined and vortexed for five seconds and incubated at 37° C. for 15 minutes.
  • the sample was incubated for 5 minutes at 37° C., placed in the MR Reader (see Example 6) to measure the T 2 relaxation rate of the sample, and the T 2 relaxation rate of the sample was compared to a standard curve (see FIG. 29 ) to determine the concentration of tracrolimus in the liquid sample.
  • Example 6 Several identical samples were prepared as described in Example 6. All samples were placed into the gMAA unit for 1 minute. All samples were then placed into a tray removed from the magnetic field. Each sample was vortexed for at least five seconds and returned to the tray. All samples were again placed into the gMAA unit for 1 minute. This process was repeated twelve times for each sample, to obtain replicate measurements.
  • the sample was vortexed for 5 seconds, incubated for 5 minutes at 37° C., and placed in the MR Reader to measure the T 2 relaxation rate of the sample.
  • control is gMAA (magnet exposure+vortex, repeat) in which the relative position of the sample and the magnetic field direction are unchanged with each cycle;
  • twist is gMAA (magnet exposure+rotation within magnet, repeat) with rotating tube ca. 90° relative to the gradient magnet with each cycle;
  • 180 turn is gMAA (magnet exposure+remove tube from magnet, rotate, place back in magnet, repeat) with rotating tube ca. 180° relative to the gradient magnet with each cycle;
  • the liquid sample is exposed to magnetic fields from different directions in an alternating fashion.
  • the rate at which a steady state degree of agglomeration, and stable T 2 reading, is achieved is expedited by cycling between the two or more positions over a series of gMAA treatments.
  • FIG. 27 A standard curve for the competitive creatinine creatinine assay with alternating side-bottom gMAA is shown in FIG. 27 demonstrating good response with the side-bottom gMAA configuration.
  • Samples were prepared by adding 20 ⁇ L of varied concentrations of Protein A (a target protein) and 20 ⁇ L Anti-Protein A antibody coated magnetic particles at 0.08 mM Fe to a PCR Tube (1.2 ⁇ 10 9 particles per tube). Samples were placed into a 32 position tray, vortexed in a plate shaker for 2 minutes at 2000 rpm and incubated in a 37° C. incubation station for 15 minutes.
  • a fixed magnet time of 6 minutes with the following dwell times was also evaluated: 30, 60, 120 seconds.
  • Samples were prepared by adding 20 ⁇ L of varied concentrations of Protein A (a target protein) and 20 ⁇ L Anti-Protein A antibody coated magnetic particles at 0.08 mM Fe to a PCR Tube (1.2 ⁇ 10 9 particles per tube). Samples were placed into a 32 position tray, vortexed in a plate shaker for 2 minutes at 2000 rpm and incubated in
  • T 2 response is directly proportional to temperature and dwell time. Therefore, increased temperature and dwell time/total time results in improved T 2 response.
  • two pools of magnetic particles are used for detection of each Candida species.
  • a species specific Candida capture oligonucleotide probe is conjugated to the magnetic particles.
  • an additional species-specific capture oligonucleotide probe is conjugated to the magnetic particles.
  • the two particles will hybridize to two distinct species-specific sequences within the sense strand of the target nucleic acid, separated by approximately 10 to 100 nucleotides.
  • the two capture oligonucleotides can be conjugated to a single pool of particles, resulting in individual particles having specificity for both the first and second regions).
  • the oligonucleotide-decorated magnetic particles are designed to aggregate in the presence of nucleic acid molecules from a particular species of Candida .
  • the Candida assay features an increase in agglomeration in the presence of the target Candida nucleic acid molecules.
  • the hybridization-mediated agglomerative assay architecture is depicted in FIG. 32 .
  • Carboxylated magnetic particles are used in the Candida assays. Magnetic particles were conjugated to oligonucleotide capture probes to create oligonucleotide-particle conjugates. For each target amplicon, two populations of oligonucleotide-particle conjugates were prepared. Oligonucleotide-particle conjugates were prepared using standard EDC chemistry between aminated oligonucleotides and carboxylated particles, or, optionally, by coupling biotin-TEG modified oligonucleotides to streptavidin particles. Coupling reactions were typically performed at a particle concentration of 1% solids.
  • oligonucleotide densities were measured by hybridizing Cy5-labeled complements to the particles, washing the particles three times to remove non-hybridized oligo; and eluting by heating to 95° C. for 5 minutes.
  • the amount of Cy5 labeled oligonucleotide was quantified via fluorescence spectroscopy.
  • the coupling reactions were performed at 37° C. overnight with continuous mixing using a rocker or roller.
  • the resulting particle conjugates were washed twice with 1 ⁇ reaction volume of Millipore water; twice with 1 ⁇ reaction volume of 0.1 M Imidazole (pH 6.0) at 37° C. for 5 minutes; three times with 1 ⁇ reaction volume of 0.1 M sodium bicarbonate at 37° C. for 5 minutes; then twice with 1 ⁇ reaction volume of 0.1 M sodium bicarbonate at 65° C. for 30 minutes.
  • the resulting particle conjugates were stored at 1% solids in TE (pH 8), 0.1% Tween®20).
  • the panel of Candida species detected includes C. albicans, C. glabrata, C. krusei, C. tropicalis , and C. parapsilosis .
  • the sequences are amplified using universal primers recognizing highly conserved sequence within the genus Candida .
  • the capture oligonucleotides were designed to recognize and hybridize to species-specific regions within the amplicon.
  • the mixture is subjected to PCR cycles: 62° C. annealing; 68° C. elongation; 95° C.—for 40 cycles. Note: there is a 6° C. difference in the annealing and elongation temperatures; the annealing and elongation may be combined into a single step to reduce the total amplification turn-around time.
  • the PCR amplicon now ready for detection, is combined with two populations of particles in a sandwich assay.
  • PCR primers and capture probes which can be used in the Candida assay are provided below in Table 8.
  • Candida krusei AAG TTC AGC GGG TAT TCC TAC Probe #2 CT (SEQ ID NO. 6) Candida krusei probe AGC TTT TTG TTG TCT CGC AAC ACT CGC (SEQ ID NO. 32) Candida glabrata CTA CCA AAC ACA ATG TGT TTG Probe #1 AGA AG (SEQ ID NO. 7) Candida glabrata CCT GAT TTG AGG TCA AAC TTA Probe #2 AAG ACG TCT G (SEQ ID NO. 8) Candida parapsilosis / AGT CCT ACC TGA TTT GAG GTC tropicalis NitInd 1 AA (SEQ ID NO.
  • NitInd is 5′ 5-Nitroindole, a base that is capable of annealing with any of the four DNA bases. 2 Note that oligo Ts are added as spacers
  • the assay is carried out in the presence of a control sequence, along with magnetic particles decorated with probes for confirming the presence of the control sequence.
  • the aminosilane-treated nickel metal foam was treated with 2% gluteraldehyde in water for 2 hours at room temp and washed extensively with deionized water. Next, the metal foam was exposed to 100 ⁇ g/ml of anti-creatinine antibody (14HO3) (see Example 6) in PBS overnight, washed extensively with PBS, and treated with Surmodics Stabilguard to stabilize and block non-specific binding. Two mm square pieces of the derivatized metal foam were cut using a fresh razor blade being careful not to damage the foam structure.
  • the PCR tube containing the derivatized metal foam and control particles was placed in a gMAA fixture (side pull 6 position) for one minute and removed touched with a hand demagnetizer, and placed back into the gMAA fixture for another minute, removed touched with a hand demagnetizer and placed back into the gMAA fixture for another minute and vortexed (three 1 minute magnetic exposures).
  • Thirty ⁇ l of sample was removed from both PCR tubes, heated to 37° C. in a grant block heater for 5 minutes and the T 2 read using the MR Reader (see Example 6).
  • the derivatized metal foam was de-magnetized, vortexed and rinsed in assay buffer. It was placed in a new PCR tube with 20 ⁇ l of assay buffer and 20 ⁇ l of AACr2-3-4 particles derivatized with creatinine with a final particle concentration of 0.1 mMFe. A duplicate PCR tube without the derivatized metal foam was also set up as in the control experiment. The PCR tube with the metal foam was cycled twice through the gMAA device exactly as the control experiment (3 one minute exposures with demag after each exposure, and final vortex). Thirtly ⁇ l samples from both tubes were removed and heated to 37° C. for 5 minutes and then read on the MR reader.
  • T 2 measurements could detect single nucleotide polymorphisms.
  • thermophilic DNA ligase Tth ligase
  • This assay would require lysis of the sample material followed by DNA shearing. Adaptors could be ligated onto the sheared DNA if a universal amplification of the genomic DNA was needed.
  • the SNP would be detected by engineering superparamagnetic particle bound capture probes which flank the SNP such that the 5′ end of the 3′ aminated capture probe would be perfectly complementary to one particular SNP allele and subsequent treatment with Tth ligase would result in the ligation of the two particle-bound capture probes. Ligation would therefore lock the particles into an agglomerated state.
  • Tth polymerase has been demonstrated to have superior discrimination capability even discriminating G-T mismatches (a particular permissive mismatch and also the most common) 1:200 fold against the correct complement.
  • ligase detection reactions as well as oligonucleotide ligase assays have been employed in the past to define nucleotide sequences at known polymorphic sites, all required amplification either before or after ligation; in this particular example the signal could be amplified via a ligation induced increase in the size of the resulting agglomerated particle complex and thereby increases in the measured relaxation times (T 2 ).
  • a modification to this procedure could include hybridization of a particle bound capture probe flanking the hybridization of a biotinylated probe.
  • the ligase would covalently bind the biotin probe to the magnetic particle. Again repeated rounds of heat denaturation followed by annealing and ligation should yield a high proportion of long biotinylated oligos on the magnetic particle surface.
  • a wash to remove any free probe would be conducted followed by the addition of a second streptavidin labeled superparamagnetic particle. Agglomeration would ensue only if the biotinylated probes were ligated onto the surface of first particle.
  • a hybridization discrimination approach could as well be employed.
  • aminated oligonucleotide complements adjacent to known SNPs would be generated. These aminated oligonucleotides would be used to derivatize the surface of a 96-well plate with 1 SNP detection reaction conducted per well. Genomic DNA would then be sheared, ligated to adaptors, and asymmetrically amplified. This amplified genomic DNA would then be applied to the array as well as a short biotinylated SNP detecting probe. The amplified genomic DNA would hybridize to the well-bound capture probe and the SNP detecting probe would then bind to the tethered genomic DNA. Washing would be conducted to remove free SNP-detecting probe.
  • a streptavidin (SA) magnetic particle would then be added to each well. Washing again would be required to remove free-SA particles.
  • T 2 detection could be conducted directly within the wells by added biotinylated superparamagnetic particles to yield surface tethered agglomerated particles, or the SA magnetic particles could be eluted from each well on the array and incubated in detection reactions with biotinylated magnetic particles.
  • a primer extension reaction could be coupled to T 2 detection to discriminate which nucleotide is present at a polymorphic site.
  • a pool of dideoxynucleotides would be employed with one nucleotide per pool possessing a biotin (i.e., ddA, ddT, ddbiotin-C, and/or ddG).
  • a superparamagnetic particle bearing a capture probe whose last base upon hybridization lies adjacent to a SNP would be employed.
  • the sheared genomic DNA would be split and incubated in four separate primer extension reactions.
  • An exo-DNA polymerase would then catalyze the addition of a dideoxy complementary to the nucleotide present in the SNP. Again this reaction could be cycled if a thermophilic polymerase is employed to ensure that most of the capture probes on the particle will be extended.
  • a magnetic separation followed by a wash of the particles would be conducted followed by incubation with streptavidin superparamagnetic particles. Clustering would ensue proportional to the extent of biotinylated capture probe on the surface of the first particle. If two of the dideoxypools generated a gain in T 2 (i.e., facilitate particle agglomeration), the patient would be a heterozygote. If only one pool yielded and increase in T 2 , the patient would be a homozygote.
  • a final method to detect SNPs employs allele-specific PCR primers, in which the 3′ end of the primer encompasses the SNP. Since stringent amplification conditions are employed, if the target sequence is not perfectly complementary to the primer, PCR amplification will be compromised with little or no product generated. In general, multiple forward primers would be designed (one perfectly complementary to each allele) along with a single reverse primer. The amplicon would be detected using two or more capture probe bound superparamagnetic particles to induce hybridization based agglomeration reactions.
  • One advantage of this approach is that it leverages some of the work already conducted at T 2 on PCR within crude samples, and would merely entail primers designed to encompass known SNPs. A disadvantage in this approach is that it cannot determine de novo SNP locations.
  • An additional method which can be used is simply relying on the discrimination capabilities of particle-particle cross-linking due to hybridization to a short nucleic acid target. Mismatches in base pairs for oligonucleotides have been shown to dramatically shift the agglomeration state of particles, and the measured T 2 signal, due to reduced hybridization efficiencies from the presence of a single base mismatch.
  • C. albicans and C. krusei reference strains as well as C. albicans clinical isolates were cultivated and maintained for the duration of the study.
  • C. albicans and C. krusei nanoparticles Two particle populations were generated for each species, the particles bearing covalently conjugated to oligos complementary to species-specific sequences within the ITS2 region (see Example 14). The particles were stored at 4-8° C. in TE (pH 8), 0.1% Tween and were diluted to 0.097 mM Fe in DNA hybridization buffer immediately before use.
  • Candida strains Panels were performed using C. albicans reference strain MYA 2876 (GenBank FN652297.1), C. krusei reference strain 24210 (GenBank AY939808.1), and C. albicans clinical isolates. The five C. albicans isolates used were cultivated on YPD at room temperature. Single colonies were selected, washed 3 times with PBS, and then quantified via hemocytometer for preparation of whole blood spikes. The samples were stored as frozen glycerol stocks as ⁇ 80° C.
  • Erythrocyte Lysis buffer A hypotonic lysis buffer containing 10 mM potassium bicarbonate, 155 mM ammonium chloride, and 0.1 mM EDTA was filter sterilized and stored at room temperature prior to use.
  • an erythrocyte lysis agent can be used, such as a non-ionic detergent (e.g., a mixture of Triton-X 100 and igepal, or Brij-58).
  • PCR master mix A master mix containing buffer, nucleotides, primers, and enzyme was prepared (20 ⁇ L 5 ⁇ reaction buffer, 22 ⁇ L water, 2 ⁇ L 10 mM dNTP, 3 ⁇ L 10 ⁇ M forward primer, 3 ⁇ L 2.5 ⁇ M reverse primer, 10 ⁇ L HemoKlenTaq, and 40 ⁇ L bead beaten lysate) and stored at room temperature.
  • Particle hybridization master mix A master mix consisting of nanoparticle conjugates, salts, surfactant, and formamide was prepared (78 ⁇ L formamide, 78 ⁇ L 20 ⁇ SSC, 88.3 ⁇ L 1 ⁇ TE+0.1% Tween, 7.5 ⁇ L CP 1-3′, and 8.2 ⁇ L CP 3-5′) immediately before use.
  • FIG. 47 A general scheme of the workflow for detection of a pathogen (e.g., Candida ) in a whole blood sample is shown in FIG. 47 .
  • the protocol was as follows: (i) human whole blood spiked samples were allowed to warm to room temperature ( ⁇ 30 minutes); (ii) 1 mL of erythrocyte lysis buffer was aliquoted into each tube; (iii) each tube was centrifuged at 9000 g for 5 minutes and the lysed blood discarded; (iv) 100 ⁇ L of 0.2 micron filtered TE was aliquoted into each tube; (v) 120 mg of acid washed glass beads were added to each tube; (vi) each tube was vortexed for 3 minutes at maximum speed ( ⁇ 3000 rpm); (vii) 50 ⁇ L of lysed sample was aliquoted into a tube containing PCR master mix (viii) cycle PCR reactions as follows: (initial denaturation: 95° C., 3 minutes; 30-40 cycles at 95° C
  • FIG. 46A The within run precision is shown in FIG. 46A and in general is tight with the CV's of all measurands less than 12%.
  • the repeatability observed over the course of eight days is shown in FIG. 46B with the CVs less than 10% across the range of Candida concentrations and 6% for the negative control.
  • a two population two-tailed Student's T-test was applied to determine if the difference in means between the mock Candida infected blood at 10 cells/mL and the healthy donor blood was significant. The results are summarized in Table 9.
  • Candida albicans clinical isolates were spiked into 6 different donor blood samples at concentrations of 1E4, 1E3, 5E2, 1E2, 50, 10, 5, and 0 cells/mL. Each isolate was spiked into a minimum of two different donor blood samples. Amplification reactions were detected via T 2 measurement with the results plotted in FIG. 49 . It is important to note that no data was removed for cause within this study. We did not detect C. albicans 50% of the time at 5 cells/mL or 10 cells/mL; however at 50 cells/mL C. albicans was detected 95% of the time.
  • Table 10A shows the time from inoculation to culture positive recorded for four different C. albicans clinical isolates inoculated into blood culture.
  • C. albicans 100 25 12 isolate CFU/mL CFU/mL CFU/mL 0.0 0.0 C1 739.0 409.0 632.5 112.7 112.8 C2 983.2 1014.5 997.6 117.4 114.8 C3 912.7 510.5 113.3 116.2 112.0 C4 807.6 741.2 665.2 119.1 115.9
  • Clinical accuracy is defined as the ability to discriminate between two or more clinical states, for example Candidemia versus no Candidemia.
  • Receiver Operator Characteristic (ROC) plots describe the test's performance graphically illustrating the relationship between sensitivity (true positive fraction) and specificity (true negative fraction). The clinical accuracy (sensitivity/specificity pairs) is displayed for the entire spectrum of decision levels. Using the data generated from the 10 cells/mL and 50 cells/mL clinical isolate spiked whole blood samples, two ROC plots were generated and are shown in FIGS. 50A and 50B .
  • the area under the curve is often used to quantify the diagnostic accuracy; in this case our ability to discriminate between a Candidemic patient with an infection of 10 cells/mL or 50 cells/mL versus a patient with no Candidemia.
  • the area under the curve is 0.72 which means that if the T 2 assay was run on a randomly chosen person with Candidemia at a level of infection of 10 cells/mL, there is an 72% chance their T 2 value would be higher than a person with no Candidemia.
  • the clinical accuracy of the test is much higher at 50 cells/mL with the area under the curve at 0.98.
  • the T 2 assay would give a value higher than a sample from a patient without Candidemia 98% of the time. This is excellent clinical accuracy for infection levels of 50 cells/mL. ROC plots were not prepared for the 100 cells/mL samples or higher as the area would be translating to 100% clinical diagnostic accuracy. Final clinical accuracy is determined from real patient samples on the clinical platform.
  • the primary assay steps with estimated times are: (i) hypotonic lysis/centrifugation/bead beating (8 min); (ii) PCR (120 min.); (iii) hybridization of amplicon to particles (30 min.); (iv) hMAA (10 min.); and (v) transfer and read (10 sec.).
  • the processing time for the assay is estimated at ⁇ 178 minutes ( ⁇ 3 hrs), excluding reagent and equipment preparation. This is the workflow used for qualification; however we have demonstrated that the following modified work-flow with shorter PCR and hybridization steps does yield the same detection sensitivity (see FIG.
  • This testing demonstrates a current T 2 based molecular diagnostic assay for Candidemia with the following metrics: (i) detection of Candida albicans within whole blood at a range spanning 5-1E5 cells/mL (5-log); (ii) detection of Candida krusei within whole blood at a range spanning 10 cells/mL to 1E5 cells/mL; (iii) sensitivity/specificity of 100%/100% at >25 cells/mL; (iv) diagnostic accuracy of greater than 98% for concentrations >50 cells/mL; (v) assay compatibility with whole blood (no major matrix effects observed using twelve different donor blood samples); (vi) repeatability of T 2 measurements (less than 12% within the same day and less than 13% across eight days); and (vii) reduced total assay turnaround time to 2 hours 3 minutes.
  • PCR steps may be separated from the detection steps.
  • chemical/biochemical methods may be used to render the amplicons unamplifiable.
  • uracils may be incorporated into the PCR product, and a pre-PCR incubation may be conducted with uracil N glycosylase.
  • the advantages of the systems and methods of the invention include the ability to assay whole blood samples without separating proteins and non-target nucleic acids from the sample. Because no losses in target nucleic acids are incurred through DNA purification (e.g., running Qiagen column after lysis and prior to amplification results in >10 ⁇ loss in sensitivity; and use of whole blood interferes with optical detection methods at concentrations above 1%), sample-to-sample variability and biases (which can be introduced by DNA purification) are minimized and sensitivity is maximized.
  • CMV genomic DNA was spiked into CMV-free healthy donor blood samples, 40 ⁇ L of this spiked blood was aliquoted into a 100 ⁇ L total volume PCR reaction. Amplification was conducted using a whole blood compatible thermophilic DNA polymerase (T2 Biosystems, Lexington, Mass.) and exemplary universal primers that were designed as follows: 24 mer end—C6 linker—CMV specific sequence, the exact sequences were as follows:
  • the primers were designed such that the capture probes (i.e., the nucleic acid decorating the magnetic particle) would anneal to the 10mer region (10mers are different on either 5′ or 3′ end).
  • the final primer concentration in the reaction tube was 300 nM and PCR master mix which included 5 mM (NH 4 ) 2 SO 4 , 3.5 mM MgCl 2 , 6% glycerol, 60 mM Tricine (pH 8.7)).
  • Five separate sample reaction tubes were set up. Cycle PCR reactions followed an initial denaturation of 95° C. for 3 minutes, and each cycle consisted of 95° C., 20 seconds; 55° C., 30 seconds; and 68° C., 20 seconds.
  • reaction tubes were removed and maintained at 4° C.
  • 5 ⁇ L of particle master mix (6 ⁇ SSC, 30% formamide, 0.1% Tween) was aliquoted into the tube for every 10 ⁇ L of amplified sample; the resulting mixture was well mixed and the sample denatured at 95° C. for 3 minutes; the sample was hybridized at 45° C. for 1 hour with gentle agitation; the sample was then diluted to 150 ⁇ L with particle dilution buffer (PBS, 0.1% Tween, 0.1% BSA), placed into a temperature controlled hMAA magnet for 10 minutes, and equilibrated to 37° C. in a heat block for 1 minute; and the T 2 relaxation time for each of the five separate samples was measured using a T 2 MR reader (see FIG. 52 ).
  • PBS particle dilution buffer
  • the primers were designed to allow the magnetic particles decorated with capture probes to anneal to the 10mer region (10mers are different on either 5′ or 3′ end), providing particles with a universal architecture for aggregation with specific amplification primers.
  • results provided in FIG. 52 show that the methods and systems of the invention can be used to perform real time PCR and provide quantitative information about the amount of target nucleic acid present in a whole blood sample.
  • a simple magnetic separator/PCR block insert ( FIG. 53 ) was designed to keep nanoparticles on the side walls during PCR reaction, thus minimizing interference and particle exposure to the PCR reaction components. Upon removal of the magnetic field, particles can be completely resuspended into the reaction mixture.
  • PCR was performed under two conditions: (1) nanoparticles are fully dispersed in solution; and (2) nanoparticles are concentrated on the PCR test tube side walls using magnetic insert.
  • the assay can include an internal control nucleic acid that contains primer binding regions identical to those of the target sequence.
  • the target nucleic acid and internal control are selected such that each has a unique probe binding region that differentiates the internal control from the target nucleic acid.
  • the internal control can be an inhibition control that is designed to co-amplify with the nucleic acid target being detected. Failure of the internal inhibition control to be amplified is evidence of a reagent failure or process error.
  • Universal primers can be designed such that the target sequence and the internal control sequence are amplified in the same reaction tube. Thus, using this format, if the target DNA is amplified but the internal control is not it is then assumed that the target DNA is present in a proportionally greater amount than the internal control and the positive result is valid as the internal control amplification is unnecessary. If, on the other hand, neither the internal control nor the target is amplified it is then assumed that inhibition of the PCR reaction has occurred and the test for that particular sample is not valid.
  • the already amplified and detected Candida albicans sequence was examined for use in generating an internal control.
  • the universal primer sequences were removed from the 5′ and 3′ ends.
  • the residual internal sequence was subjected to a random sequence generator and a random sequence was generated.
  • the universal primer sequences were replaced at the ends and the full internal control sequence was cloned into pCR2.1-TOPO and was sequence verified.
  • the following criteria and features for use in diagnostic PCR assays were employed: 1) the target and internal control DNA share the same primers; 2) the internal control and target DNA are easily distinguishable (i.e. different capture probes); 3) the amplification efficiencies of the target and internal control have been tested and are acceptable; 4) the source of the internal control is a plasmid DNA carrying the cloned internal control sequence; 5) the internal control is detected by sequence dependent hybridization; 6) the internal control plasmid is highly purified; 7) the concentration of the internal control is determined by titration; 8) the internal control plasmid is added to the PCR mix to ensure equal distribution to all of the PCR tubes; 9) it has been determined the amount of internal control in the assay reaction tubes is 100-1000 copies/reaction and this concentration has been determined to be the lowest amount that still elicits a signal via amplification. See Hoofar et al., J. Clin. Microbiol. 42:1863 (2004).
  • the internal inhibition control for the Candida assay was designed to co-amplify with the Pan Candida PCR primers and contain a unique intervening sequence of similar length and base composition as the Candida species.
  • the intervening sequence was developed by applying a sequence randomizing algorithm to the C. ablicans amplicon sequence. Four randomized sequences were then thermodynamically and bioinformatically characterized. A nucleotide megaBLAST search was conducted for each sequence using both the human genomic+transcript database as well as the nr database. No significant alignments were identified with the four query sequences in either database. Each sequence was then subjected to UNAfold analysis to determine the extent of secondary structure present at the hybridization concentration of monovalent cation (600 mM) at a temperature of 60 degrees C.
  • the annealed complementary sequence is:
  • 5 uM of the annealed duplex in 2 ⁇ SSC was sent to SeqWright for subcloning and sequencing.
  • the annealed duplexes contain 3′ adenosine overhangs to facilitate cloning into a TA cloning vector.
  • This construct was cloned into pCR2.1-TOPO.
  • 5 clones were selected and sequenced to confirm the presence of the correct insert.
  • the mini-prepped plasmid DNA should be digested with EcoRV and HindIII and the insert subcloned into pBR322. From this transformation, 5 transformants were selected and the insert verified via sequencing.
  • Two E. coli hosts bearing the pBR322-IC were frozen in 30% glycerol+LB amp.
  • a plasmid maxi-prep was conducted using the Qiagen and yielded ⁇ 1 mg of purified plasmid DNA.
  • Capture probes were designed to hybridize nested to the Pan Candida PCR primer sequences.
  • a 3′ aminated capture probe with a T-9 linker was designed to complementary to the 5′ end of the strand amplified in excess.
  • a 5′ aminated capture probe with a C12 T-9 linker was designed complementary to the 3′ end of the strand amplified in excess.
  • the predicted melting temperatures (Allawi, 1997) were 75 and 78° C., respectively.
  • FIG. 56A Three prototype rotary gMAA configurations were designed, built and tested with comparison to the conventional plate based gMAA (see FIG. 56A ).
  • the three configurations included varying magnetic field exposures—side-bottom; side-null and bottom-null.
  • the plate based gMAA used for comparison is the standard side-bottom.
  • Assay functional performance was evaluated using the Creatinine agglomerative assay system. Particles derivatized with creatinine antibody were mixed with 1:5 diluted serum and creatinine dextran agglomerator. The agglomerator was tested at 6 concentrations to provide a titration curve. Each concentration level was tested in triplicate. The T2 of samples with no agglomerator was measured before and after gMAA to assess non-specific binding.
  • gMAA was performed at room temperature for a total of 12 minutes with 1 minute dwells at the magnet stations.
  • Example 22 Candida Assay and Clinical Data
  • a rapid, accurate, and reproducible molecular diagnostic test was developed for the detection of five Candida species directly within human whole blood with a limit of detection (LOD) of 10 cells/mL and a time to result of less than 2 hours.
  • LOD limit of detection
  • the assay's clinical performance was determined using 32 blinded clinical specimens and in this study we observed 100% positive and 100% negative agreement with blood culture while accurately identifying the causative Candida species within 100% of the candidemic patient samples.
  • This diagnostic method is rapid, amenable to automation, and offers clinicians the opportunity to detect multiple human pathogens within complex biological specimens.
  • MR magnetic resonance
  • This system was held at 37° C. via temperature control and contains a samarium cobalt permanent magnet of approximately 0.5 T, corresponding to a proton frequency of operation of 22-24 MHz. All standard MR components: radio frequency probe, low-noise pre-amplifier and transmitter electronics, spectrometer board, as well as the temperature control hardware are packaged in the system.
  • the system uses standard AC power input and connects to an external computer via Ethernet.
  • a user friendly graphical user interface allows users to set experimental parameters.
  • the system has been designed to accept samples in standard 0.2 ml PCR tubes.
  • the electronics as well as the coil were optimized to improve the measurement precision of the applicable sample volumes, allowing us to achieve single-scan run to run CVs in T2 of less than 0.1%.
  • Instrument to instrument variability is under 2% with minimal tolerance requirements on the system components and without calibration.
  • 800 nm carboxylated iron oxide superparamagnetic particles consisting of numerous iron oxide nanocrystals embedded in a polymer matrix including a total particle diameter of 800 nm (see Demas et al., New J. Phys. 13:1 (2011)), were conjugated to aminated DNA oligonucleotides using standard carbodiimide chemistry. DNA-derivatized nanoparticles were stored at 4° C. in 1 ⁇ Tris-EDTA (pH 8), 0.1% Tween-20.

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